17-44372199-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_000419.5(ITGA2B):c.*165T>C variant causes a 3 prime UTR change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: ITGA2B NM_000419.5 3_prime_UTR
• Clinical Significance: Uncertain significance reviewed by expert panel U:1
• Conservation: PhyloP100: 4.07

Genes affected

ITGA2B (HGNC:6138): (integrin subunit alpha 2b) This gene encodes a member of the integrin alpha chain family of proteins. The encoded preproprotein is proteolytically processed to generate light and heavy chains that associate through disulfide linkages to form a subunit of the alpha-IIb/beta-3 integrin cell adhesion receptor. This receptor plays a crucial role in the blood coagulation system, by mediating platelet aggregation. Mutations in this gene are associated with platelet-type bleeding disorders, which are characterized by a failure of platelet aggregation, including Glanzmann thrombasthenia. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2B	NM_000419.5	c.*165T>C		3_prime_UTR_variant	30/30	ENST00000262407.6
ITGA2B	XM_011524749.2	c.*165T>C		3_prime_UTR_variant	29/29
ITGA2B	XM_011524750.2	c.*165T>C		3_prime_UTR_variant	29/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2B	ENST00000262407.6	c.*165T>C		3_prime_UTR_variant	30/30	1	NM_000419.5	P1
ITGA2B	ENST00000587295.5	c.*165T>C		3_prime_UTR_variant	3/3	3
ITGA2B	ENST00000648408.1	c.*165T>C		3_prime_UTR_variant	25/25

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 6

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Glanzmann thrombasthenia Uncertain:1

Uncertain significance, reviewed by expert panel

curation

ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen

Jun 02, 2022

The NM_000419.5(ITGA2B):c.*165T>C 3'UTR variant was identified homozygous (PM3_supporting) in at least one patient (GT75 in PMID: 25728920) who displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, alphaIIbbeta3 surface expression was reduced to <5%, as measured by flow cytometry (PP4_strong). This variant is absent from gnomAD v3.1.2 (PM2_Supporting). ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PP4_strong, PM2_supporting, PM3_supporting. (VCEP specifications version 2.1). These criteria reach Likely Pathogenic however, to our knowledge, there is no known disease mechanism for 3'UTR variants in Glanzmann thrombasthenia. In the absence of additional cases or functional data the ClinGen PD VCEP classifies this variant as uncertain significance for autosomal recessive Glanzmann Thrombasthenia. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	18
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-42449567;