The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000552.5(VWF):c.391G>A (p.Gly131Ser)

CA6403810

256677 (ClinVar)

Gene: VWF
Condition: hereditary von Willebrand disease
Inheritance Mode: Undetermined mode of inheritance
UUID: f186bfc7-d6a5-4e9b-8dfd-c592e28854ab
Approved on: 2024-08-12
Published on: 2024-08-12

HGVS expressions

NM_000552.5:c.391G>A
NM_000552.5(VWF):c.391G>A (p.Gly131Ser)
NC_000012.12:g.6110515C>T
CM000674.2:g.6110515C>T
NC_000012.11:g.6219681C>T
CM000674.1:g.6219681C>T
NC_000012.10:g.6089942C>T
NG_009072.1:g.19156G>A
NG_009072.2:g.19156G>A
ENST00000261405.10:c.391G>A
ENST00000261405.9:c.391G>A
ENST00000321023.5:c.*450G>A
ENST00000538635.5:n.420G>A
NM_000552.3:c.391G>A
NM_000552.4:c.391G>A

Likely Benign

Met criteria codes 2
BP4 BS1
Not Met criteria codes 1
BS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen von Willebrand Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VWF Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
von Willebrand Disease VCEP
NM_000552.5:c.391G>A is a missense variant in VWF that replaces glycine with serine at position 131. The Grpmax filtering allele frequency in gnomAD v4.1 is 0.02093 (based on 1636/75004 alleles in the African/African-American population), which is higher than the ClinGen VWD VCEP threshold (>0.01) for BS1, and therefore meets this criterion (BS1). This variant has been reported in the heterozygous state in at least 5 reported healthy control individuals with no bleeding history and normal lab values (PMID: 22197721). However, BS2 has not been considered since this code is not applicable to the gene-disease relationship due to incomplete penetrance. The computational predictor REVEL gives a score of 0.141, which is below the ClinGen VWD VCEP threshold of <0.290 and does not predict a damaging effect on VWF function (BP4). Additionally, the computational splicing predictor SpliceAI indicated that the variant has no impact on splicing. In summary, this variant meets the criteria to be classified as a variant of unknown significance for hereditary von Willebrand disease based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: BS1, BP4.
Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.141, which is below the ClinGen VWD VCEP threshold of <0.290 and does not predict a damaging effect on VWF function (BP4). Additionally, the computational splicing predictor SpliceAI gives a score of 0.06 for splice acceptor gain, indicating that the variant likely has no impact on splicing.
BS1
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.02093 (based on 1636/75004 alleles in the African/African-American population), which is higher than the ClinGen VWD VCEP threshold (>0.01) for BS1, and therefore meets this criterion (BS1).
Not Met criteria codes
BS2
At least 5 reported healthy control individuals with no bleeding history and normal lab values harbored the variant in the heterozygous state (PMID: 22197721). BS2 has not been considered since this code is not applicable to the gene-disease relationship due to incomplete penetrance.
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