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.2220G>A (p.Met740Ile)

CA201316

100206 (ClinVar)

Gene: VWF
Condition: hereditary von Willebrand disease
Inheritance Mode: Undetermined mode of inheritance
UUID: 6c4fcdfa-5916-4b27-a95f-8a5f89a9c41b
Approved on: 2024-07-09
Published on: 2024-08-12

HGVS expressions

NM_000552.5:c.2220G>A
NM_000552.5(VWF):c.2220G>A (p.Met740Ile)
NC_000012.12:g.6046784C>T
CM000674.2:g.6046784C>T
NC_000012.11:g.6155950C>T
CM000674.1:g.6155950C>T
NC_000012.10:g.6026211C>T
NG_009072.1:g.82887G>A
NG_009072.2:g.82887G>A
ENST00000261405.10:c.2220G>A
ENST00000261405.9:c.2220G>A
ENST00000538635.5:n.421-52850G>A
NM_000552.3:c.2220G>A
NM_000552.4:c.2220G>A
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Benign

Met criteria codes 2
BP4 BA1
Not Met criteria codes 1
BP2

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(VWF):c.2220G>A is a missense variant that replaces methionine with isoleucine at position 740. The Grpmax filtering allele frequency in gnomAD v4.1 is 0.1791 (based on 13626/75022 alleles in the African/African-American population), which is higher than the ClinGen VWD VCEP threshold (>0.1) for BA1, and therefore meets this criterion (BA1). This variant has been observed in multiple VWD Type 2M probands in cis with the NM_000552.5(VWF):c.3614G>A (p.Arg1205His) variant, with the phase of the variants confirmed by family segregation analysis (PMID: 10959712). This second variant has been classified Pathogenic for VWD Type 2M by the ClinGen VWD VCEP (BP2). The computational predictor REVEL gives a score of 0.059, 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 Likely Benign for hereditary von Willebrand disease based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: BA1, BP4.
Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.059, 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.
BA1
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.1791 (based on 13626/75022 alleles in the African/African-American population), which is higher than the ClinGen VWD VCEP threshold (>0.1) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
BP2
This variant has been observed in multiple VWD Type 2M probands in cis with the NM_000552.5(VWF):c.3614G>A (p.Arg1205His) variant, with the phase of the variants confirmed by family segregation analysis (PMID: 10959712). This second variant has been classified Pathogenic for VWD Type 2M by the ClinGen VWD VCEP, however BP2 is not used at this time.
Curation History
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