Evidence Repository
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
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000173.7(GP1BA):c.482C>T (p.Thr161Met)

CA8314782

226006 (ClinVar)

Gene: GP1BA
Condition: Bernard-Soulier syndrome
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: e31b5e95-6f91-4e53-af0a-a3bfe7e04d1d
Approved on: 2025-02-11
Published on: 2025-02-12

HGVS expressions

NM_000173.7:c.482C>T
NM_000173.7(GP1BA):c.482C>T (p.Thr161Met)
NC_000017.11:g.4933086C>T
CM000679.2:g.4933086C>T
NC_000017.10:g.4836381C>T
CM000679.1:g.4836381C>T
NC_000017.9:g.4777161C>T
NG_008767.2:g.5792C>T
ENST00000329125.6:c.482C>T
ENST00000649830.1:c.-888+1256G>A
ENST00000329125.5:c.482C>T
ENST00000611961.1:c.482C>T
NM_000173.6:c.482C>T
More

Benign

Met criteria codes 2
BA1 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GP1BA Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The missense variant NM_000173.7(GP1BA):c.482C>T (p.Thr161Met) is associated with the polymorphism HPA-2. Moreover, the Grpmax filtering allele frequency in gnomAD v4.1 is 0.2237 (based on 16982/74950 alleles) in African/African American population, which is significantly higher than the ClinGen PD VCEP threshold (>0.001) for BA1. Additionally, the computational predictor REVEL gives a score of 0.041, which is below the ClinGen PD VCEP threshold of <0.25 predicting no damaging effect on GP1BA function and the SpliceAI score is zero (BP4). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive Bernard-Soulier syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: BA1 and BP4.
Met criteria codes
BA1
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.2237 (based on 16982/74950 alleles) in African/African American population, which is significantly higher than the ClinGen PD VCEP threshold (>0.001), and therefore meets this criterion (BA1).
BP4
The computational predictor REVEL gives a score of 0.041, which is below the ClinGen PD VCEP threshold of <0.25 predicting no damaging effect on GP1BA function and the SpliceAI score is zero (BP4).
Curation History
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