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.4138A>G (p.Ile1380Val)

CA6402595

310063 (ClinVar)

Gene: VWF
Condition: hereditary von Willebrand disease
Inheritance Mode: Undetermined mode of inheritance
UUID: 33e927e5-ccc5-446d-9962-23c4eeee0df2
Approved on: 2024-11-05
Published on: 2024-11-06

HGVS expressions

NM_000552.5:c.4138A>G
NM_000552.5(VWF):c.4138A>G (p.Ile1380Val)
NC_000012.12:g.6019280T>C
CM000674.2:g.6019280T>C
NC_000012.11:g.6128446T>C
CM000674.1:g.6128446T>C
NC_000012.10:g.5998707T>C
NG_009072.1:g.110391A>G
NG_009072.2:g.110391A>G
ENST00000261405.10:c.4138A>G
ENST00000261405.9:c.4138A>G
ENST00000538635.5:n.421-25346A>G
NM_000552.3:c.4138A>G
NM_000552.4:c.4138A>G
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Benign

Met criteria codes 3
BA1 BP5 BP4
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
The NM_000552.5:c.4138A>G variant in VWF is a missense variant predicted to cause substitution of isoleucine by valine at amino acid 1380. The Grpmax filtering allele frequency in gnomAD v4.1 is 0.1164 (based on 8878/74958 alleles in the African/African American population, including 541 homozygotes), which is higher than the ClinGen VWD VCEP threshold of >0.1 for BA1. This variant has been observed in 1 VWD Type 2B patient with an alternate molecular basis for disease, the presence (with unreported phase) of the p.Arg1341Gln variant, previously classified Pathogenic for VWD Type 2B by the ClinGen VWD Type 2 VCEP (BP5; PMID: 30817071). At least 16 healthy adult individuals harboring the p.Asn1435Ser variant were found to be unaffected, with no diagnosis of a bleeding disorder and normal lab values, including bleeding scores lower than 4, VWF:RCo/VWF:Ag ratios >0.6, and no increased response to low-dose ristocetin (PMID: 20231421). The mean VWF:RCo/VWF:Ag ratio of 0.71-0.77 within this group was significantly reduced compared to 0.91-0.97 for WT, but within the normal range. However, BS2 was not considered due to incomplete penetrance in this gene-disease relationship. The computational predictor REVEL gives a score of 0.098, 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 is classified as Benign for hereditary von Willebrand disease based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: BA1, BP4, BP5.
Met criteria codes
BA1
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.1164 (based on 8878/74958 alleles in the African/African American population, including 541 homozygotes), which is higher than the ClinGen VWD VCEP threshold of >0.1 for BA1.
BP5
This variant has been observed in 1 patient with an alternate molecular basis for disease, the presence (with unreported phase) of the p.Arg1341Gln variant, previously classified Pathogenic by the ClinGen VWD Type 2B VCEP (BP5; PMID: 30817071).
BP4
The computational predictor REVEL gives a score of 0.098, 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 0.00 for all splicing types, indicating that the variant has no impact on splicing.
Not Met criteria codes
BS2
At least 16 healthy adult individuals harboring the p.Asn1435Ser variant were found to be unaffected, with no diagnosis of a bleeding disorder and normal lab values, including bleeding scores lower than 4, VWF:RCo/VWF:Ag ratios >0.6, and no increased response to low-dose ristocetin (PMID: 20231421). The mean VWF:RCo/VWF:Ag ratio of 0.71-0.77 was significantly reduced compared to 0.91-0.97 for WT but above the threshold of <0.6. BS2 is not considered for this gene-disease relationship due to incomplete penetrance.
Curation History
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