Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
ERBB4
Final classification
VUS
ERBB4 c.2371A>G · p.Thr791Ala
ERBB4

NM_005235.2:c.2371A>G (p.Thr791Ala) is a missense variant in exon 20 of ERBB4. It is present at extremely low frequency in population databases (gnomAD v2.1: 3/251,416 alleles, AF=0.00119%; gnomAD v4.1: 24/1,614,034 alleles, AF=0.00149%) with no homozygotes observed, meeting PM2 at supporting strength.

Gene
ERBB4
Transcript
NM_005235.2
HGVS · transcript:coding
NM_005235.2:c.2371A>G
Consequence
N/A
GRCh38
chr2:211562019 T>C
GRCh37
chr2:212426744 T>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
ERBB4 c.2371A>G

NM_005235.2:c.2371A>G (p.Thr791Ala) is a missense variant in exon 20 of ERBB4. It is present at extremely low frequency in population databases (gnomAD v2.1: 3/251,416 alleles, AF=0.00119%; gnomAD v4.1: 24/1,614,034 alleles, AF=0.00149%) with no homozygotes observed, meeting PM2 at supporting strength.1 Multiple computational predictors support a benign interpretation: REVEL score of 0.321 is below the pathogenic threshold, BayesDel score of -0.090 is in the benign range, and SpliceAI predicts no splice impact (max delta = 0.00). BP4 is met at supporting strength.2 This variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (LabCorp, Ambry Genetics), each with criteria provided as a single submitter. No expert panel review has been performed.3 No functional studies, segregation data, de novo observations, case-control studies, or family co-segregation data are available for this variant. The variant lies within the ERBB4 kinase domain but is not located in a recognized mutational hotspot.4 Applying the generic ACMG/AMP 2015 final classification rules (PMID:25741868): one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) result in an overall classification of Uncertain Significance. The evidence is balanced and insufficient to classify this variant as either likely pathogenic or likely benign.5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_005235.2 · variants mapped to exon structure
ERBB4 NM_005235.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present at extremely low frequency in population databases. gnomAD v2.1 reports 3/251,416 alleles (AF=0.00119%) and gnomAD v4.1 reports 24/1,614,034 alleles (AF=0.00149%), both well below the 0.1% threshold. No homozygotes are observed. gnomAD-Canada v1.0 reports the variant as absent.
gnomAD v2.1: AF=0.00119% (3/251416 alleles0 hom)
BP4 supporting Benign
Multiple lines of computational evidence support a benign effect. REVEL score is 0.321 (below the pathogenic threshold of 0.5), BayesDel score is -0.090 (negative, consistent with a benign interpretation), and SpliceAI predicts no splice impact (max delta score = 0.00).
REVEL: 0.321 (below 0.5 pathogenic threshold)BayesDel: -0.0903471 (benign range)SpliceAI: max delta=0.00 (no predicted splice alteration).
Assessed · not applied
Pathogenic
PS1 No alternate nucleotide change resulting in the same amino acid substitution (p.Thr791Ala) has been reported as pathogenic.
PS2 No de novo occurrence of NM_005235.2:c.2371A>G with confirmed paternity and maternity has been reported in the literature or variant databases.
PS3 No well-established functional studies have been performed to assess the damaging effect of p.Thr791Ala.
PS4 No case-control studies have compared the prevalence of NM_005235.2:c.2371A>G in affected individuals versus general population controls.
PM1 Although p.Thr791 resides within the ERBB4 protein kinase domain (residues 712–989), the variant is not located in a statistically significant mutational hotspot.
PM6 No presumed de novo occurrence (without confirmation of paternity and maternity) has been reported for NM_005235.2:c.2371A>G in the literature or variant databases.
PP1 No co-segregation data are available.
PP2 There is insufficient evidence that ERBB4 meets the PP2 criteria: a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No phenotypic data are available for the individual(s) carrying this variant.
PP5 No reputable source has classified this variant as pathogenic.
Benign
BA1 The maximum population allele frequency for NM_005235.2:c.2371A>G is 0.00801% in the African/African American subpopulation (gnomAD v4.1), far below the BA1 threshold of 1%.
BS1 The maximum population allele frequency for NM_005235.2:c.2371A>G is 0.00801% (gnomAD v4.1 African/African American), well below the BS1 threshold of 0.3%.
BS2 No homozygous individuals have been observed in gnomAD (v2.1 or v4.1).
BS3 No well-established functional studies demonstrating a neutral or benign effect of p.Thr791Ala on protein function have been identified.
BS4 No segregation data are available to evaluate lack of segregation in affected family members.
BP1 ERBB4 is not established as a gene where only truncating variants cause disease.
BP2 No observation of NM_005235.2:c.2371A>G in trans with a pathogenic variant in a gene for a fully penetrant dominant disorder, nor in cis with a pathogenic variant in any inheritance pattern, has been reported.
BP5 No case has been reported in which NM_005235.2:c.2371A>G is found in an individual with an alternate molecular basis for disease.
BP6 No reputable source has classified this variant as benign.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.48696e-05; MAF= 0.00149%, 24/1614034 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 8.00747e-05; MAF= 0.00801%, 6/74930 alleles, homozygotes = 0); grpmax FAF= 3.471e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.19324e-05; MAF= 0.00119%, 3/251416 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.63764e-05; MAF= 0.00264%, 3/113738 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0015% · 24 / 1,614,034
0 hom · FAF 0.0035%
African/African American
6 / 74,930
0.008%
European (non-Finnish)
18 / 1,180,036
0.0015%
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
0.0012% · 3 / 251,416
0 hom · FAF 0.0007%
European (non-Finnish)
3 / 113,738
0.0026%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 3063763)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.321. BayesDel score = -0.0903471.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. ERBB4, a receptor tyrosine kinase, is altered at low to moderate frequencies in various cancer types, most frequently in melanoma and lung cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 12 PMIDs not cited in assessment
23619275 ↗ ACMG position statement on prenatal/preconception expanded carrier screening. CLINVAR
23652378 ↗ A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document. CLINVAR
25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
23169492 ↗ The perspective from EASAC and FEAM on direct-to-consumer genetic testing for health-related purposes. CLINVAR
24121147 ↗ Appropriateness of newborn screening for α1-antitrypsin deficiency. CLINVAR
22947299 ↗ Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening. CLINVAR
23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR
23881473 ↗ Newborn screening: education, consent, and the residual blood spot. The position of the national society of genetic counselors. CLINVAR
24022298 ↗ Offering prenatal diagnostic tests: European guidelines for clinical practice [corrected]. CLINVAR
24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR
31022120 ↗ ACOG Committee Opinion No. 778 Summary: Newborn Screening and the Role of the Obstetrician-Gynecologist. CLINVAR