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.346C>T (p.Leu116Phe)

CA8622917

890134 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: e4ad6f4d-1b93-4ead-8729-f651137791cf

HGVS expressions

NM_000212.3:c.346C>T
NM_000212.3(ITGB3):c.346C>T (p.Leu116Phe)
NC_000017.11:g.47283534C>T
CM000679.2:g.47283534C>T
NC_000017.10:g.45360900C>T
CM000679.1:g.45360900C>T
NC_000017.9:g.42715899C>T
NG_008332.2:g.34693C>T
ENST00000559488.7:c.346C>T
ENST00000559488.5:c.346C>T
ENST00000560629.1:c.311C>T
ENST00000571680.1:c.346C>T
NM_000212.2:c.346C>T

Uncertain Significance

Met criteria codes 1
PP3
Not Met criteria codes 4
BP2 BA1 PM2 BS1

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The c.346C>T variant in ITGB3 is a missense variant predicted to cause substitution of Leucine by Phenylalanine at amino acid 116 (p.Leu116Phe). The highest population minor allele frequency in gnomAD v4.0.0 is 0.0003737 (28/74930 alleles) in the African/African American population. This intermediate allele frequency is lower than the ClinGen PD VCEP threshold (>0.00158) for BS1 but higher than the threshold (<0.0001) for PM2_Supporting. The computational predictor REVEL gives a score of 0.773, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on function (PP3). This variant was observed as part of a predisposition screen in an ostensibly healthy population by Illumina. This variant is also reported in ClinVar in a heterozygous, Portuguese female, presenting with autosomal dominant macrothrombocytopenia (Unidade de Genética Molecular, Centro Hospitalar Universitário do Porto; SCV002540771.1). The only case of this variant occurring in autosomal recessive Glanzmann thrombasthenia (PMID: 27469266) was in a patient with an alternate explanation for disease, compound heterozygous for c.861del and c.1456del (both classified Pathogenic by the PD-VCEP). In summary, this variant meets the criteria to be classified as VUS for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PP3 (VCEP specifications version 2).
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.773, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on function (PP3).
Not Met criteria codes
BP2
This variant was reported (PMID: 27469266) as a heterozygous polymorphism in a GT patient compound heterozygous for c.861del and c.1456del (both classified Pathogenic by the PD-VCEP). However, no confirmation of phasing was provided so theoretically both frameshifts could be on the same allele and this variant on the opposite allele.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
The highest population minor allele frequency in gnomAD v4.0.0 is 0.0003737 (28/74930 alleles) in the African/African American population. This intermediate allele frequency is lower than the ClinGen PD VCEP threshold (>0.00158) for BS1 but higher than the threshold (<0.0001) for PM2_Supporting.
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-12-19
Published on: 2023-12-19
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.