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_000212.3(ITGB3):c.261C>G (p.Ala87=)

CA8622902

889447 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: 79a36fcb-780d-430b-82a2-c3df79fca120

HGVS expressions

NM_000212.3:c.261C>G
NM_000212.3(ITGB3):c.261C>G (p.Ala87=)
NC_000017.11:g.47283449C>G
CM000679.2:g.47283449C>G
NC_000017.10:g.45360815C>G
CM000679.1:g.45360815C>G
NC_000017.9:g.42715814C>G
NG_008332.2:g.34608C>G
ENST00000696963.1:c.261C>G
ENST00000559488.7:c.261C>G
ENST00000559488.5:c.261C>G
ENST00000560629.1:c.226C>G
ENST00000571680.1:c.261C>G
NM_000212.2:c.261C>G

Likely Benign

Met criteria codes 3
PM2_Supporting BP4 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2.1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
After a comprehensive literature search of the synonymous variant NM_000212.3(ITGB3):c.261C>G (p.Ala87=), no individuals with Glanzmann thrombasthenia were reported with the variant and has only been observed in a ostensibly healthy population. The variant has a minor allele frequency of 0.00006 (1/16256 alleles) in the African/African American population in gnomAD, which meets the threshold criteria for PM2_supporting. In silico predictor spliceAI revealed that the synonymous mutation is not expected to impact splicing and a PhyloP score of 1.32 shows that the nucleotide position is not highly conserved (BP4, BP7). Due to conflicting evidence, this variant is classified as likely benign for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD-VCEP: PM2_Supporting, BP4, BP7. (PD VCEP specifications version 2.1).
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006 (1/16256 alleles) in the African/African American population, which is lower than the ClinGen PD VCEP threshold (<0.0001; PM2_Supporting).
BP4
The c.261C>G (p.Ala87=) variant is a synonymous variant that is not predicted by SpliceAI to impact splicing (BP4).
BP7
The c.261C>G (p.Ala87=) variant is a synonymous variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by PhyloP score of 1.32 (BP7).
Approved on: 2024-03-07
Published on: 2024-03-08
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