Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_000174.5(GP9):c.18C>T (p.Ala6=)

CA2602623

902701 (ClinVar)

Gene: GP9 (HGNC:2815)

Condition: Bernard-Soulier syndrome (MONDO:0009276)

Inheritance Mode: Autosomal recessive inheritance

UUID: e4127e2c-fa98-4675-9431-a74187085d18

Approved on: 2026-01-20

Published on: 2026-01-20

HGVS expressions

NM_000174.5(GP9):c.18C>T (p.Ala6=)

NM_000174.5:c.18C>T

NC_000003.12:g.129061757C>T

CM000665.2:g.129061757C>T

NC_000003.11:g.128780600C>T

CM000665.1:g.128780600C>T

NC_000003.10:g.130263290C>T

NG_008715.1:g.5956C>T

ENST00000307395.5:c.18C>T

ENST00000307395.4:c.18C>T

NM_000174.4:c.18C>T

Benign

BA1 BP4 BP7

Evidence Links 0

Expert Panel

Platelet Disorders VCEP

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GP9 Version 1.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Platelet Disorders VCEP

The c.18C>T (p.Ala6=) variant in GP9 is a synonymous variant that is not predicted by SpliceAI to impact splicing (score <0.1). In addition, it occurs at a nucleotide that is not highly conserved as shown by phyloP score of -0.7486 (BP7 and BP4). The Grpmax Filtering allele frequency in gnomAD v4.1.0 is 0.001318 (based on 68/44866 alleles) in the South Asian population, which is higher than the ClinGen PD VCEP threshold (>0.001), and therefore meets this criterion (BA1). This variant was observed by Illumina as part of a predisposition screen in an ostensibly healthy population, however, no cases of the variant segregating in Bernard Soulier Syndrome have been found in the literature. 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, BP4 and BP7 (VCEP specifications version 1).

BA1

The Grpmax Filtering allele frequency in gnomAD v4.1.0 is 0.001318 (based on 68/44866 alleles) in the South Asian population, which is higher than the ClinGen PD VCEP threshold (>0.001), and therefore meets this criterion (BA1).

BP4

The computational splicing predictor SpliceAI indicated that the variant has no impact on splicing (score <0.1).

BP7

Curation History

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