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  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data


Variant: NM_000174.5(GP9):c.-124C>T

CA82551874

901795 (ClinVar)

Gene: GP9
Condition: Bernard-Soulier syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: bbc7d7ab-9078-4381-a1c3-3e912c351ed4
Approved on: 2025-02-11
Published on: 2025-02-14

HGVS expressions

NM_000174.5:c.-124C>T
NM_000174.5(GP9):c.-124C>T
NC_000003.12:g.129061508C>T
CM000665.2:g.129061508C>T
NC_000003.11:g.128780351C>T
CM000665.1:g.128780351C>T
NC_000003.10:g.130263041C>T
NG_008715.1:g.5707C>T
ENST00000307395.5:c.-124C>T
ENST00000307395.4:c.-124C>T
NM_000174.4:c.-124C>T
More

Benign

Met criteria codes 2
BA1 BP7

Evidence Links 0

Expert Panel

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.-124C>T variant in GP9 is a non-coding variant which located upstream of the 5' UTR. It was identified through an ICLS predisposition screen in an ostensibly healthy population. To date, this variant has not been reported in any patients with BSS. The c.-124C>T variant is an intronic variant that is not predicted by SpliceAI to impact splicing (acceptor gain score of 0.1 which is less than the VCEP threshold of <0.2). In addition, it occurs at a nucleotide that is not highly conserved as shown by phyloP score of 0.314583 (<1.5) (BP7). The Grpmax Filtering allele frequency in gnomAD v4.1 is 0.004120 (248/54052 alleles) in the African/African American population, which is higher than the ClinGen PD VCEP threshold (>0.001), and therefore meets this criterion (BA1). 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, BP7.
Met criteria codes
BA1
The Grpmax Filtering allele frequency in gnomAD v4.1 is 0.004120 (248/54052 alleles) in the African/African American population, which is higher than the ClinGen PD VCEP threshold (>0.001), and therefore meets this criterion (BA1).
BP7
The c.-124C>T variant is an intronic variant that is not predicted by SpliceAI to impact splicing (acceptor gain score of 0.1 which is less than the VCEP threshold of <0.2). In addition, it occurs at a nucleotide that is not highly conserved as shown by phyloP score of 0.314583 (<1.5) (BP7).
Curation History
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