The HBB NM_000518.5:c.20A>T (NP_000509.1:p.(Glu7Val)) missense variant has not previously been reported in somatic cancers (COSMIC). Experimental evidence: Double-mutant hemoglobin containing c.20A>T had P50 43.0 versus 24.0 mm Hg for HbS with 3.0 mM DPG, but isolated-variant attribution is limited. Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.HBB encodes the beta-globin protein, one of the two types of chains that combine with alpha-globin to form adult hemoglobin, which carries oxygen in the blood. Abnormal or absent beta-globin is associated with sickle cell disease and beta-thalassemia. HBB has no established cancer role.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, strong: PMID:15470216 directly identifies c.20A>T as beta-Glu6Val, the standard HbS pathogenic amino-acid change.
Met, supporting: double-mutant hemoglobin containing c.20A>T had P50 43.0 versus 24.0 mm Hg for HbS with 3.0 mM DPG, but isolated-variant attribution is limited.
No benign criterion marked as applied in the recorded assessment.
VUS: PS1 strong plus PS3 supporting does not meet a generic ACMG/AMP pathogenic, likely pathogenic, benign, or likely benign combination rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 4,272 / 1,610,650 alleles. Recorded AF 0.00265235. Recorded homozygote count 40.
This variant is present in gnomAD v2.1 (AF= 0.00437398; MAF= 0.43740%, 1236/282580 alleles, homozygotes = 4) and has highest observed frequency in the African/African American population (AF= 0.0449047; MAF= 4.49047%, 1121/24964 alleles, homozygotes = 4); grpmax FAF= 0.0442364.
This variant is present in gnomAD-Canada v1.0 (AF= 0.005215123859191656, 96/18408 alleles, homozygotes = 11).
Recorded REVEL score: 0.535. Refer to the recorded PP3/BP4 rationale for interpretation.
59 Pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
No standalone functional evidence summary is recorded in evidence_summary.functional.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 2 met · 12 not met · 10 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The only directly relevant family report shows c.20A>T inherited from the father and distinguishes it from a different de novo HBB variant; no qualifying PP1 or BS4 family data are documented.
Population evidence does not support BA1, BS1, or PM2 under the generic rules. BS2 remains unassessed because aggregate homozygote counts do not establish a healthy adult phenotype.
The ancestry-specific high frequency is consistent with the known HbS carrier-selection pattern and must not be treated as an automatic BS1 finding from the generic 1% default alone.
No criteria match.
The investigated variant is NM_000518.5:c.20A>T, NP_000509.1:p.(Glu7Val), the canonical HbS missense change. PMID:15470216 directly identifies the same c.20A>T substitution as beta-Glu6Val, standard HbS, establishing the same amino-acid change as a previously disease-associated pathogenic variant. The paper also reports sickling-related clinical manifestations and biochemical abnormalities in a patient carrying this variant with an additional beta-Leu68Phe change; the exact same amino-acid change is sufficient for PS1, while the additional change is a caveat for interpreting the paper's functional findings.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
PS3 is met at supporting strength. PMID:15470216 explicitly identifies NM_000518.5:c.20A>T as betaGlu6Val, the standard HbS mutation, and reports functional testing involving purified HbS and a patient-derived/recombinant double-mutant hemoglobin containing betaGlu6Val plus betaLeu68Phe. The assay included oxygen-binding studies with HbS comparator, sodium chloride and 2,3-diphosphoglycerate, polymerization-solubility testing, and tetramer-stability testing. The double-mutant hemoglobin showed a P50 of 43.0 mm Hg versus 24.0 mm Hg for HbS in 3.0 mM 2,3-diphosphoglycerate and reduced anaerobic solubility, supporting impaired hemoglobin function and sickling biology. Supporting rather than stronger calibration is warranted because the principal abnormal functional measurements were obtained with the double mutant rather than an isolated c.20A>T construct, although the study directly compared it with HbS and separately identifies c.20A>T as standard HbS.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
PS2 is not met. The variant NM_000518.5:c.20A>T (p.Glu7Val; HbS) was identified in the patient's father, while the mother's HBB gene was wild-type. The report describes the de novo event as a different variant, HBB c.335C>T (p.Leu68Phe), which arose on the paternal HbS allele; therefore c.20A>T was inherited rather than de novo. The report does not establish the required de novo status for c.20A>T.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
The governing ACMG/AMP PS4 rule requires affected-person prevalence to be significantly increased versus controls and, under the supplied note, an OR or RR >5.0 with a confidence interval excluding 1.0. The literature_pass.json PS4 leads were checked against the available paper extracts: PMID:15470216 documents one patient with HbS plus a second cis mutation and does not provide an affected-versus-unaffected control comparison; PMID:21045822 reports global HbS population frequencies and malaria-associated geographic enrichment but no variant-specific affected/control case-control counts; PMID:20301608 has no abstract or full text available here; and the PMID:6268660 lead has no source-registry or paper-extract record. No case-control counts or valid OR/RR with a confidence interval were identified, so PS4 is not met.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
The variant is common in population controls rather than absent or extremely rare: default all-comers gnomAD v2.1 reports AF 0.00437398 with 4 homozygotes, and gnomAD v4.1 reports AF 0.00265235 with 40 homozygotes. The corresponding non-cancer results also show AF 0.00343557 in v2.1 exomes and AF 0.0129259 in v3.1 genomes. These values are all above the generic PM2 supporting threshold of 0.0001, so PM2 is not met.
PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)
PM6 is not met. The available family study identifies NM_000518.5:c.20A>T (p.Glu7Val; HbS) in the father, so this variant is not merely assumed to be de novo without parental confirmation. The de novo finding in the report is HBB c.335C>T (p.Leu68Phe), not c.20A>T.
Assumed de novo, but without confirmation of paternity and maternity.
The variant is a missense SNV, NM_000518.5:c.20A>T (p.Glu7Val), so the governing computational path is REVEL only; SpliceAI is not used for PP3/BP4 in this situation. REVEL is 0.535, below the generic ClinGen SVI PP3 supporting threshold of >= 0.644 (and below the moderate and strong thresholds of >= 0.773 and >= 0.932), so PP3 is not met. BayesDel is not usable because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only.
The governing rule requires a reputable recent pathogenic report whose supporting evidence is unavailable for independent evaluation. ClinVar contains a Pathogenic aggregate from clinical laboratories, but the audit records zero expert-panel submissions and no usable expert-panel assertion for this exact variant; ordinary laboratory submissions and aggregate labels do not qualify.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
The variant does not reach the generic BA1 threshold in the default all-comers gnomAD datasets: gnomAD v2.1 overall AF is 0.00437398 and the highest reported population AF is 0.0449047, while gnomAD v4.1 overall AF is 0.00265235 and the highest reported population AF is 0.0494874. Both are below 0.05. The gnomAD v3.1 non-cancer genome subset has an HGDP:YORUBA estimate of 0.184211 based on only 7/38 alleles, but this is not the default all-comers source and is too small and population-specific to override the default assessment; gnomAD-Canada also reports 0.0825147 in AFR, but is not one of the specified default datasets.
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
The generic 1% BS1 default is exceeded in the African/African American ancestry group (4.49047% in gnomAD v2.1 and 4.94874% in gnomAD v4.1), but the frequency is not greater than expected for sickle-cell disease. This HBB p.Glu7Val (HbS) allele is common in populations with historical malaria exposure because heterozygous carriers are generally clinically unaffected and balancing selection maintains the allele; the disease risk is primarily in homozygotes or compound heterozygotes. Therefore the default 1% cutoff cannot be applied in isolation, and no maximum-credible-frequency calculation with prevalence, penetrance, and allelic-heterogeneity inputs is available that would establish BS1 for this disorder.
BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)
BS3 is not met. The reviewed variant-specific functional study does not show preserved protein function or absence of damaging effect; instead, it identifies c.20A>T as the standard HbS betaGlu6Val mutation and reports abnormal oxygen binding, polymerization-related solubility, and sickling-associated biology in hemoglobin containing this variant. The study's main experimental protein was a double mutant, so it is not a basis for a stronger PS3 calibration, but it provides no evidence supporting BS3.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
BP1 is not supported because HBB has an established disease-causing missense mechanism: PMID:15470216 directly identifies the HBB beta-Glu6Val missense change as standard HbS and describes associated sickling disease. This is incompatible with treating HBB as a gene in which disease is primarily caused by truncating variants for this missense interpretation.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
The variant is a missense SNV, NM_000518.5:c.20A>T (p.Glu7Val), so the governing computational path is REVEL only; the SpliceAI result cannot substitute for a gray-zone REVEL result. REVEL is 0.535, which is above the generic ClinGen SVI BP4 supporting upper threshold of <= 0.29 and therefore does not support BP4. BayesDel is not usable because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... Missense variant -> REVEL only.
The governing rule requires a reputable recent benign report whose supporting evidence is unavailable for independent evaluation. The exact-variant ClinVar audit shows no expert-panel submission or expert-panel benign assertion, and no qualifying expert-panel benign report is present.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The hotspot evidence reports that HBB Glu7 is not in a statistically significant hotspot. The authoritative vcep_materials.json domain_tables object is empty, so no complete approved HBB critical-domain list is available for checking residue 7. Because the hotspot is negative but critical-domain status cannot be established from the available governing materials, PM1 is not assessed rather than called not met.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
PM3 cannot be assessed because the available evidence does not document NM_000518.5:c.20A>T in trans with a pathogenic variant in an affected individual, nor does it provide parental or offspring testing establishing phase. The available Hb Jamaica Plain report documents this variant in cis with p.Leu68Phe on the paternal allele, which is not PM3 evidence.
For recessive disorders, detected in trans with a pathogenic variant...Note: This requires testing of parents (or offspring) to determine phase.
The case evidence identifies p.Glu7Val but provides no verified pathogenic alternate missense substitution at residue 7. The PM5 candidate file contains zero same-residue candidates, and the reviewed paper extracts do not establish a different pathogenic HBB missense change at this residue. Therefore the required comparator evidence is unavailable.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
PP1 cannot be assessed because the available evidence does not document multiple affected family members carrying NM_000518.5:c.20A>T (p.Glu7Val), nor does it provide a meiosis count or a segregation analysis across affected relatives. The available family report shows the father carried HbS, but does not establish him or other relatives as affected with the disease under evaluation.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
The available case evidence does not provide a gene-level benign missense constraint measure or a sufficiently characterized HBB missense-versus-other-mechanism disease spectrum to establish both PP2 requirements. Variant-specific pathogenicity evidence cannot substitute for the required gene-level assessment.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
The governing rule requires a documented patient phenotype or family history highly specific for a disease with a single genetic etiology. The case evidence provides the HBB variant and literature context but does not provide an index patient's clinical phenotype, family history, or a sufficiently specific disease presentation for this criterion.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
gnomAD reports homozygotes (4 in v2.1 and 40 in v4.1), including 36 African/African American homozygotes in v4.1, but these aggregate counts do not document that any specific homozygous individual was a healthy adult without sickle-cell disease. Because BS2 requires observation in a healthy adult and the available population records provide no individual phenotype, the criterion cannot be assessed from these data.
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
BS4 cannot be assessed because no affected family members lacking NM_000518.5:c.20A>T (p.Glu7Val) are documented. The available report describes the patient's mother as wild-type and the father as carrying HbS, but it does not establish a clinically affected relative who fails to carry the variant; therefore there is no qualifying lack-of-segregation observation.
Lack of segregation in affected members of a family.
BP2 cannot be assessed because PMID:15470216 reports NM_000518.5:c.20A>T in cis with p.Leu68Phe on the paternal allele, but the extracted report does not establish p.Leu68Phe as pathogenic. The cis observation therefore does not satisfy the criterion's required pathogenic-partner condition.
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
The governing rule requires the variant to be found in a case with an alternate molecular basis for disease. The available case evidence describes HBB variant literature but does not document an affected case in which another molecular cause explains the disease instead of this variant.
Variant found in a case with an alternate molecular basis for disease.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_000518.5:c.20A>T in HBB is a missense substitution predicted to produce NP_000509.1:p.(Glu7Val). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for HBB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_000518.5:c.20A>T in HBB is a missense substitution predicted to produce NP_000509.1:p.(Glu7Val). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for HBB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_000518.5:c.20A>T in HBB is a missense substitution predicted to produce NP_000509.1:p.(Glu7Val). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for HBB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000518.5:c.20A>T in HBB is a missense substitution predicted to produce NP_000509.1:p.(Glu7Val). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for HBB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in HBB, mapped onto the exon structure of NM_000518.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| African/African American3707 / 74,908 | 0.04936 hom |
| Middle Eastern23 / 6,052 | 0.00381 hom |
| Remaining individuals216 / 62,392 | 0.00352 hom |
| Admixed American199 / 60,018 | 0.00331 hom |
| South Asian81 / 91,040 | 0.00089 |
| European (non-Finnish)46 / 1,176,872 | 3.9e-05 |
| African/African American1121 / 24,964 | 0.0454 hom |
| Admixed American76 / 35,418 | 0.0021 |
| Remaining individuals12 / 7,222 | 0.0017 |
| South Asian19 / 30,616 | 0.00062 |
| European (non-Finnish)8 / 128,960 | 6.2e-05 |
This variant is present in gnomAD v4.1 (AF= 0.00265235; MAF= 0.26523%, 4272/1610650 alleles, homozygotes = 40) and has highest observed frequency in the African/African American population (AF= 0.0494874; MAF= 4.94874%, 3707/74908 alleles, homozygotes = 36); grpmax FAF= 0.0481577.
This variant is present in gnomAD v2.1 (AF= 0.00437398; MAF= 0.43740%, 1236/282580 alleles, homozygotes = 4) and has highest observed frequency in the African/African American population (AF= 0.0449047; MAF= 4.49047%, 1121/24964 alleles, homozygotes = 4); grpmax FAF= 0.0442364.
This variant is present in gnomAD-Canada v1.0 (AF= 0.005215123859191656, 96/18408 alleles, homozygotes = 11).
The variant is a missense SNV, NM_000518.5:c.20A>T (p.Glu7Val), so the governing computational path is REVEL only; SpliceAI is not used for PP3/BP4 in this situation. REVEL is 0.535, below the generic ClinGen SVI PP3 supporting threshold of >= 0.644 (and below the moderate and strong thresholds of >= 0.773 and >= 0.932), so PP3 is not met. BayesDel is not usable because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only.
The variant is a missense SNV, NM_000518.5:c.20A>T (p.Glu7Val), so the governing computational path is REVEL only; the SpliceAI result cannot substitute for a gray-zone REVEL result. REVEL is 0.535, which is above the generic ClinGen SVI BP4 supporting upper threshold of <= 0.29 and therefore does not support BP4. BayesDel is not usable because no generic ACMG-strength calibration is established.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... Missense variant -> REVEL only.
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000518.5:c.20A>T in HBB is a missense substitution predicted to produce NP_000509.1:p.(Glu7Val). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for HBB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.535. BayesDel score = 0.000740619.
11 paper records listed. 1 cited in the classification.
Three clones revealed an adenine-to-thymine transversion at position 20 (b 20A>T) in exon 1 (corresponding to b Glu 6 Val, which is standard HbS).
Location Results, DNA sequencing paragraph; Figure 1 legend
Context Patient and parental HBB DNA sequencing, cloning and sequencing of 10 independent PCR clones, hemoglobin electrophoresis/FPLC, purified Hb Jamaica Plain oxygen-binding studies, polymerization solubility testing, tetramer-stability assays, and recombinant Hb Jamaica Plain production in yeast.
Sickle haemoglobin (HbS), a structural variant of normal adult haemoglobin, results from a single amino acid substitution at position 6 of the beta globin molecule (β 6Glu→Val)2.
Introduction, paragraph 1; Results and Discussion sections on global HbS distribution and the malaria hypothesis
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.00265235; MAF= 0.26523%, 4272/1610650 alleles, homozygotes = 40) and has highest observed frequency in the African/African American population (AF= 0.0494874; MAF= 4.94874%, 3707/74908 alleles, homozygotes = 36); grpmax FAF= 0.0481577.
This variant is present in gnomAD v2.1 (AF= 0.00437398; MAF= 0.43740%, 1236/282580 alleles, homozygotes = 4) and has highest observed frequency in the African/African American population (AF= 0.0449047; MAF= 4.49047%, 1121/24964 alleles, homozygotes = 4); grpmax FAF= 0.0442364.
This variant is present in gnomAD-Canada v1.0 (AF= 0.005215123859191656, 96/18408 alleles, homozygotes = 11).
This variant has been reported in ClinVar as Pathogenic (59 clinical laboratories). (ClinVarID = 15333)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.535. BayesDel score = 0.000740619.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.