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

Variant: NM_000212.3(ITGB3):c.180C>T (p.Gly60=)

CA8622889

697901 (ClinVar)

Gene: ITGB3
Condition: Glanzmann's thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 18621042-73cc-4e74-b3cb-b35c400f1ece
Approved on: 2021-05-07
Published on: 2021-08-20

HGVS expressions

NM_000212.3:c.180C>T
NM_000212.3(ITGB3):c.180C>T (p.Gly60=)
NC_000017.11:g.47283368C>T
CM000679.2:g.47283368C>T
NC_000017.10:g.45360734C>T
CM000679.1:g.45360734C>T
NC_000017.9:g.42715733C>T
NG_008332.2:g.34527C>T
ENST00000696963.1:c.180C>T
ENST00000559488.7:c.180C>T
ENST00000559488.5:c.180C>T
ENST00000560629.1:c.145C>T
ENST00000571680.1:c.180C>T
NM_000212.2:c.180C>T
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Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 3
BS1 BS2 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
NM_000212.3(ITGB3):c.180C>T (p.Gly60=) synonymous variant was observed by Illumina as part of a predisposition screen in an ostensibly healthy population and has been reported in the literature in a blood donor cohort (PMID: 32110192) but has not been reported in a GT patient. It is not predicted to have an impact on splicing and occurs at an intermediate allele frequency of 0.0007519 (15/19950 alleles) in the gnomAD East Asian population. In summary this variant meets criteria to be classified as likely benign. GT-specific criteria applied: BP4 and BP7.
Met criteria codes
BP7
The intronic variant is not predicted to impact the splice consensus sequence, according to MaxEntScan or SpliceAI. The nucleotide is not highly conserved (phyloP score -0.693504).
BP4
The intronic variant is not predicted to impact the splice consensus sequence, according to MaxEntScan or SpliceAI. CADD RawScore 0.363053 PHRED 5.013
Not Met criteria codes
BS1
This variant occurs at an intermediate allele frequency, with an overall allele frequency in gnomAD of 0.00003983 and a MAF of 0.0007519 (15/19950 alleles) in the East Asian population. This is below the BS1 threshold of >0.00158 but above the PM2 threshold of <0.0001.
BS2
Two individuals were identified with the variant (PMID: 32110192) in the sample cohort of blood and platelet donors, however full genotypes were not provided and no clinical information was available to confirm that individuals are not affected with GT.
PM2
This variant occurs at an intermediate allele frequency, with an overall allele frequency in gnomAD of 0.00003983 and a MAF of 0.0007519 (15/19950 alleles) in the East Asian population. This is below the BS1 threshold of >0.00158 but above the PM2 threshold of <0.0001.
Curation History
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