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_000212.3(ITGB3):c.1143A>T (p.Val381=)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA8623176

890709 (ClinVar)

Gene: ITGB3

Condition: Glanzmann thrombasthenia

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 71b09e7f-4b6b-46fa-97aa-a963dac008cf

Approved on: 2023-09-07

Published on: 2023-09-21

HGVS expressions

NM_000212.3:c.1143A>T

NM_000212.3(ITGB3):c.1143A>T (p.Val381=)

NC_000017.11:g.47290971A>T

CM000679.2:g.47290971A>T

NC_000017.10:g.45368337A>T

CM000679.1:g.45368337A>T

NC_000017.9:g.42723336A>T

NG_008332.2:g.42130A>T

ENST00000559488.7:c.1143A>T

ENST00000559488.5:c.1143A>T

ENST00000560629.1:c.1108A>T

ENST00000571680.1:c.1143A>T

NM_000212.2:c.1143A>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 Version 2.1

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Platelet Disorders VCEP

The c.1143A>T (p.Val381=) 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 -0.329 (BP7). The computational predictor REVEL predicts no damaging effect on ITGB3 function (BP4). The highest population minor allele frequency in gnomAD v2.1.1 is 0.006167 (123/19946 alleles) in the East Asian population, which is higher than the ClinGen PD VCEP threshold (>0.0024) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: BP7, BP4 and BA1 (VCEP specifications version 2).

BA1

The highest population minor allele frequency in gnomAD v2.1.1 is 0.006167 (123/19946 alleles) in the East Asian population, which is higher than the ClinGen PD VCEP threshold (>0.0024) for BA1, and therefore meets this criterion (BA1).

BP4

The c.1143A>T (p.Val381=) variant is a synonymous variant that is not predicted by SpliceAI to impact splicing.

BP7

Curation History

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