The CYP3A5 NM_000777.5:c.219-237A>G (NP_000768.1:p.?) intronic variant has not previously been reported in somatic cancers (COSMIC). Experimental evidence: Independent studies linked the variant to abnormal splicing, absent or reduced CYP3A5, and 18-fold lower catalytic activity in *3/*3 kidneys (P = 0.0137). Based on available guidelines, this variant is considered to be Benign.
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.CYP3A5 encodes a cytochrome P450 enzyme that helps metabolize medicines and steroid hormones such as testosterone and progesterone. Differences in CYP3A5 activity among people can affect drug processing and have been associated with susceptibility to hypertension. No established role in cancer is known.
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: independent studies linked the variant to abnormal splicing, absent or reduced CYP3A5, and 18-fold lower catalytic activity in *3/*3 kidneys (P = 0.0137).
Met, stand-alone: gnomAD v4.1 grpmax FAF 0.931362 exceeds the BA1 threshold of 0.05, with a qualifying large population represented.
Met, strong: gnomAD v4.1 grpmax FAF 0.931362 is far above the generic BS1 threshold of 0.01 and is not a small-isolate-only signal.
Met, supporting: intronic-variant SpliceAI max delta 0.00 meets the <=0.1 BP4 supporting threshold.
Benign: BA1 stand-alone benign is met, supported by BS1 strong and BP4 supporting; PS3 strong alone does not satisfy a pathogenic combination rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 1,150,440 / 1,304,936 alleles. Recorded AF 0.881606. Recorded homozygote count 522108.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
1 association. ClinVar API review status: no assertion criteria provided.
No standalone functional evidence summary is recorded in evidence_summary.functional.
This variant has not previously been reported in somatic cancers (COSMIC).
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: 4 met · 5 not met · 10 not assessed · 9 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
All three requested criteria are not applicable under the generic ACMG/AMP definitions because this is a noncanonical intronic single-nucleotide variant rather than a listed null variant, protein-length-changing indel/stop-loss, or repetitive-region in-frame indel.
None of PS2, PM6, PP1, or BS4 is assigned because the available evidence lacks a disease-relevant proband or family-based parental, segregation, or non-segregation data.
PMID:15492926 was reviewed for segregation relevance; it is a population study of CYP3A5*3 and does not provide the required clinical pedigree evidence.
Under generic ACMG/AMP rules, PS4 is not met because the exact-variant literature provides population frequencies without disease case-control enrichment, PP4 and BP5 are not assessed because required case-level phenotype or alternate-molecular-basis information is absent, and PP5/BP6 are not met because ClinVar has no exact-variant expert-panel pathogenic or benign assertion.
The only full-text paper extraction relevant to this group, PMID:15492926, was used directly for the PS4 assessment and documents population genotyping and frequencies rather than a disease case-control comparison.
The variant is intronic, so PP3 and BP4 use the SpliceAI path only; BP7 is outside scope because it applies only to synonymous variants.
SpliceAI max delta 0.00 supports BP4 at supporting strength and does not meet the PP3 supporting threshold.
Population evidence supports BA1 stand-alone and BS1 strong from the gnomAD v4.1 filtering allele frequency; PM2 is not met, and BS2 remains unassessed because the required fully penetrant early-onset disorder context is absent.
No criteria match.
PS3 is met at strong strength. Two independent human functional studies directly evaluated the CYP3A5*3 allele corresponding to NM_000777.5:c.219-237A>G. Hustert et al. studied 183 Caucasian liver samples using CYP3A5-specific Western blotting with recombinant protein calibration standards and found the g.6986A allele in all 18 high-expression livers and none of 165 low-expression livers; the authors identified loss of a cryptic intron 3 splice site as the mechanism. Givens et al. studied renal microsomes from 21 organ donors and found at least eightfold higher CYP3A5 protein and 18-fold higher CYP3A catalytic activity in *1/*3 versus *3/*3 samples, with P = 0.0001 and P = 0.0137, respectively; CYP3A4 was not detected with a specific antibody. These concordant splice, protein-expression, and enzyme-activity results are biologically relevant and include genotype-defined comparators and assay controls, supporting a damaging effect of the variant on CYP3A5 expression and function.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
BA1 is met. gnomAD v4.1 reports a filtering grpmax FAF of 0.931362, far above the generic BA1 threshold of 0.05. The frequency is not based on the Amish popmax point estimate alone: the large NFE group has 1,026,314 observed alleles and an allele frequency of 0.932930, satisfying the minimum population-size safeguard. ClinVar reports association, drug-response, and risk-factor submissions without assertion criteria, not a pathogenic consensus that would require withholding a stand-alone benign call.
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)
BS1 is met at strong strength. The reported filtering grpmax FAF is 0.931362, greatly exceeding the generic BS1 default threshold of 0.01, and the frequency is broadly high rather than confined to a small founder population. The available record describes a common CYP3A5 pharmacogenetic risk-factor/drug-response allele rather than a fully penetrant Mendelian disorder; therefore no disease-specific maximum-credible-frequency calculation can replace the generic threshold, but the observed FAF exceeds it by approximately two orders of magnitude. Whiffin et al. 2017 is cited as the framework for disease-specific maximum credible frequency, not as an unsupported numeric substitute.
BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)
The variant is intronic (NM_000777.5:c.219-237A>G), so the governing computational path is SpliceAI only; REVEL is not applicable and cannot be substituted. SpliceAI max delta is 0.00, meeting the supplied generic ClinGen SVI BP4 supporting threshold of <=0.1 (Jaganathan et al. 2019, PMID:30661751), so BP4 is met at supporting strength.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
The governing ACMG/AMP PS4 requirement is a significantly increased prevalence in affected individuals compared with controls, with Note 1 specifying OR or RR >5.0 and a confidence interval excluding 1.0. The literature_pass ai_classified_papers contain no paper classified as PS4. The relevant full-text extraction for PMID:15492926 was checked: it reports CYP3A5*3 (the exact variant) genotyped in 1,064 individuals from 52 worldwide population samples and gives population allele frequencies, but it does not report affected patients versus unaffected/population controls for a disease phenotype, case counts, an OR/RR, or a confidence interval. Therefore no case-control enrichment meeting PS4 is established.
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.
PM2 is not met. Although the variant is absent from gnomAD v2.1, it is present at very high frequency in gnomAD v4.1: total AF=0.881606 from 1,150,440/1,304,936 alleles, 522,108 homozygotes, and grpmax FAF=0.931362. This is neither absent nor extremely rare in controls and is far above the supplied PM2 threshold of <=0.0001.
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
The variant is intronic (NM_000777.5:c.219-237A>G), so the governing computational path is SpliceAI only; REVEL is not applicable and cannot be substituted. SpliceAI max delta is 0.00, below the PP3 supporting threshold of >=0.2 from the supplied generic ClinGen SVI calibration (Jaganathan et al. 2019, PMID:30661751), so PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
The governing PP5 rule requires a reputable source to recently report the variant as pathogenic when the evidence is unavailable for independent evaluation. The exact ClinVar record has no expert-panel submission, no pathogenic or likely pathogenic classification, and no assertion criteria; its classifications are association, risk factor, and drug response. The reviewed literature describes functional effects of CYP3A5*3 but does not constitute an exact-variant expert-panel pathogenic classification. PP5 is therefore not met.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
The governing BP6 rule requires a reputable source to recently report the variant as benign when the evidence is unavailable for independent evaluation. The exact ClinVar record has no expert-panel submission, no benign or likely benign classification, and no assertion criteria; it reports association, risk factor, and drug response. No exact-variant expert-panel benign assertion is present, so BP6 is not met.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The available case evidence does not document a proband with the relevant disease, absence of family history, or confirmed maternity and paternity. The literature reviewed describes population pharmacogenetic variation rather than a de novo clinical case. Therefore, the PS2 requirements cannot be evaluated.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
PM3 cannot be assessed because the available evidence does not establish a recessive disorder context, an affected proband, a pathogenic variant in trans, or parent/offspring testing to determine phase. The exact variant is described as the CYP3A5*3 intronic allele in population and functional literature, but no family-level allelic observation or phase result is reported. The ClinVar record is an association/risk-factor record without an assertion of a recessive Mendelian disorder and provides no trans-phase evidence.
PM3: For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.
The available case evidence does not document an assumed de novo occurrence, a disease-relevant proband, or parental testing. The available literature describes population allele frequencies and functional consequences, not an assumed de novo clinical observation. Therefore, PM6 cannot be evaluated.
Assumed de novo, but without confirmation of paternity and maternity.
No affected family members, variant-positive relatives, meioses, or phenotype-linked segregation results are documented. PMID:15492926 reports unrelated population samples rather than affected pedigrees. The required segregation evidence is therefore unavailable.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
The governing PP4 requirement concerns the patient's phenotype or family history. The available case evidence identifies an exact ClinVar association/risk-factor record involving salt-sensitive hypertension susceptibility, tacrolimus response, and refractory myasthenia gravis, but supplies no patient phenotype, family history, or documented phenotype specificity for a disease with a single genetic etiology. The criterion cannot be assessed from the available case-level information.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 is not assessed. gnomAD v4.1 reports 522,108 homozygotes, including 396 in the Amish group, but the criterion requires an observed healthy adult in a disorder for which full penetrance is expected at an early age. The available evidence describes CYP3A5 pharmacogenetic association, risk-factor, and drug-response contexts, not a defined fully penetrant early-onset disorder with an established inheritance model. A population homozygote count alone does not establish the required healthy-adult observation.
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.
BS3 is not assessed. The reviewed studies evaluated the variant's abnormal splicing, reduced CYP3A5 protein expression, and reduced catalytic activity; they did not provide well-established functional evidence showing no damaging effect on protein function or splicing. The absence of a benign functional assay cannot be converted into BS3.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
No affected relatives with documented absence of the variant are reported, so lack of segregation cannot be established. PMID:15492926 is a population study and does not provide a family-based non-segregation analysis for this variant.
Lack of segregation in affected members of a family.
BP2 cannot be assessed because no family, proband, or molecular observation documents this variant in trans with a pathogenic variant in a fully penetrant dominant disorder or in cis with a pathogenic variant. The available ClinVar association/risk-factor record and population/functional literature do not provide cis/trans phase information or an affected-proband observation involving a pathogenic allele.
BP2: 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 BP5 rule requires the variant to be found in a case with an alternate molecular basis for disease. The available records do not provide a disease case with an independently established alternate molecular cause; the ClinVar record is an association/risk-factor record and does not supply such case-level evidence. BP5 cannot be assessed.
Variant found in a case with an alternate molecular basis for disease.
NM_000777.5:c.219-237A>G is an intronic single-nucleotide variant in exon/intron annotation 3i, not a nonsense, frameshift, canonical +/−1 or 2 splice-site, initiation-codon, or single/multi-exon deletion variant. Variant-specific evidence reports incorrectly spliced mRNA and a nonfunctional protein, but the generic PVS1 rule does not include noncanonical intronic splice-region SNVs; therefore PVS1 is not applicable rather than downgraded.
PVS1: Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease.
PS1 is not applicable because NM_000777.5:c.219-237A>G is an intronic variant with no amino-acid change to compare; the rule is restricted to a same amino-acid change and cautions against changes acting through splicing rather than at the amino-acid/protein level.
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.
PM1 is not applicable because this intronic variant has no protein residue that can be located in a mutational hotspot or critical functional domain; the generic rule addresses location in such protein-level regions.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
NM_000777.5:c.219-237A>G is an intronic single-nucleotide substitution with predicted protein consequence NP_000768.1:p.?. It is neither an in-frame insertion/deletion nor a stop-loss variant, so it lies outside the variant types named by PM4.
PM4: Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.
PM5 is not applicable because NM_000777.5:c.219-237A>G is intronic and does not produce an amino-acid residue at which a different pathogenic missense change could be compared; the rule also cautions against splice-impact changes.
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.
PP2 is not applicable because this is an intronic rather than missense variant, so the rule's missense-variant applicability condition is not met.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
BP1 is not applicable because this is an intronic rather than missense variant, so the rule's missense-variant applicability condition is not met.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
NM_000777.5:c.219-237A>G is an intronic single-nucleotide substitution, not an in-frame deletion or insertion. Because BP3 is limited to in-frame deletions/insertions in repetitive regions without a known function, this variant is outside BP3's applicability.
BP3: In frame-deletions/insertions in a repetitive region without a known function.
The variant is intronic (NM_000777.5:c.219-237A>G), not synonymous, so it lies outside BP7's governing scope. BP7 is therefore not_applicable without evaluating conservation or splice-prediction evidence for this criterion.
A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
Every interpreted variant in CYP3A5, mapped onto the exon structure of NM_000777.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Amish851 / 912 | 0.93396 hom |
| European (non-Finnish)957479 / 1,026,314 | 0.93446634 hom |
| European (Finnish)29237 / 31,400 | 0.9313618 hom |
| Ashkenazi Jewish17686 / 19,120 | 0.938180 hom |
| Middle Eastern3390 / 3,748 | 0.91536 hom |
| Remaining individuals42047 / 48,942 | 0.8618368 hom |
| Admixed American22713 / 28,914 | 0.798988 hom |
| East Asian24370 / 33,052 | 0.748987 hom |
| South Asian33091 / 45,452 | 0.7312319 hom |
| African/African American19576 / 67,082 | 0.293082 hom |
This variant is present in gnomAD v4.1 (AF= 0.881606; MAF= 88.16065%, 1150440/1304936 alleles, homozygotes = 522108) and has highest observed frequency in the Amish population (AF= 0.933114; MAF= 93.31140%, 851/912 alleles, homozygotes = 396); grpmax FAF= 0.931362.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
The variant is intronic (NM_000777.5:c.219-237A>G), so the governing computational path is SpliceAI only; REVEL is not applicable and cannot be substituted. SpliceAI max delta is 0.00, meeting the supplied generic ClinGen SVI BP4 supporting threshold of <=0.1 (Jaganathan et al. 2019, PMID:30661751), so BP4 is met at supporting strength.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
The variant is intronic (NM_000777.5:c.219-237A>G), so the governing computational path is SpliceAI only; REVEL is not applicable and cannot be substituted. SpliceAI max delta is 0.00, below the PP3 supporting threshold of >=0.2 from the supplied generic ClinGen SVI calibration (Jaganathan et al. 2019, PMID:30661751), so PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
The variant is intronic (NM_000777.5:c.219-237A>G), not synonymous, so it lies outside BP7's governing scope. BP7 is therefore not_applicable without evaluating conservation or splice-prediction evidence for this criterion.
A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
7 paper records listed. 3 cited in the classification.
variant g.6986A (No. 18, Table 2) showed the highest specificity as a marker of the increased CYP3A5 expression since it was present in all 18 HE livers and in none of the 165 LE livers. ... The underlying mechanism involves the abolishment of a cryptic splice site in intron 3 with the resulting stabilization of CYP3A5 transcripts.
Location Results, paragraph beginning 'Using the recently determined sequence of the CYP3A locus'; Discussion
Context 183 Caucasian liver samples; variant screening by PCR amplification and sequencing; CYP3A5-specific Western blotting of liver homogenates or microsomes; recombinant CYP3A5 and other protein standards used for calibration; high-expression and low-expression liver groups were compared.
those from *1/*3 individuals had at least eightfold higher mean kidney microsomal CYP3A5 content and 18-fold higher mean CYP3A catalytic activity than did those from *3/*3 individuals (P = 0.0001 and P = 0.0137, respectively).
Location Abstract; Fig. 1 legend and Methods; Results paragraph beginning 'The average CYP3A5 content'
Context Renal microsomes from 21 organ donors were compared by CYP3A5-specific Western blotting and midazolam 1'-hydroxylation; genotype was determined by direct genomic DNA sequencing. The study included *1/*3 and *3/*3 genotype groups, Wilcoxon testing, a defined limit of quantitation, and CYP3A4-specific antibody testing.
This variation is largely due to a single-base substitution in intron 3 of CYP3A5, which results in an incorrectly spliced mRNA and a nonfunctional protein (Kuehl et al. 2001).
Location Introduction, paragraph 3
Context CYP3A5*3 was genotyped in 1,064 individuals from 52 worldwide HGDP-CEPH population samples using a CYP3A5-specific mismatch PCR-based RFLP assay with nested PCR, DdeI digestion, and agarose-gel visualization.
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= 0.881606; MAF= 88.16065%, 1150440/1304936 alleles, homozygotes = 522108) and has highest observed frequency in the Amish population (AF= 0.933114; MAF= 93.31140%, 851/912 alleles, homozygotes = 396); grpmax FAF= 0.931362.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as association (1 clinical laboratory). (ClinVarID = 5066)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
This variant has not previously been reported in somatic cancers (COSMIC).