17-44372407-CG-GC

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_000419.5:c.3076_3077delinsGC results in a missense change, Arg1026Ala. The variant is absent gnomAD v2.1.1 and v3. PMID:12575292 reports on the variant, but the evidence does not meet GT criteria for phenotype or functional studies. In summary, there is insufficient evidence at this time to classify this variant. GT-specific criteria met: PM2_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA915940802/MONDO:0010119/011

Frequency

Genomes: not found (cov: 31)

Consequence

ITGA2B
NM_000419.5 missense

Scores

Not classified

Clinical Significance

Uncertain significance reviewed by expert panel U:1

Conservation

PhyloP100: 4.08
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ITGA2BNM_000419.5 linkuse as main transcriptc.3076_3077delinsGC p.Arg1026Ala missense_variant 30/30 ENST00000262407.6
ITGA2BXM_011524749.2 linkuse as main transcriptc.3127_3128delinsGC p.Arg1043Ala missense_variant 29/29
ITGA2BXM_011524750.2 linkuse as main transcriptc.3112_3113delinsGC p.Arg1038Ala missense_variant 29/29

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ITGA2BENST00000262407.6 linkuse as main transcriptc.3076_3077delinsGC p.Arg1026Ala missense_variant 30/301 NM_000419.5 P1P08514-1
ITGA2BENST00000587295.5 linkuse as main transcriptc.269_270delinsGC p.Arg91Ala missense_variant 3/33
ITGA2BENST00000648408.1 linkuse as main transcriptc.2390_2391delinsGC p.Arg798Ala missense_variant 25/25

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Glanzmann thrombasthenia Uncertain:1
Uncertain significance, reviewed by expert panelcurationClinGen Platelet Disorders Variant Curation Expert Panel, ClinGenNov 02, 2023The NM_000419.5:c.3076_3077delinsGC results in a missense change, Arg1026Ala. The variant is absent gnomAD v2.1.1 and v3. PMID: 12575292 reports on the variant, but the evidence does not meet GT criteria for phenotype or functional studies. In summary, there is insufficient evidence at this time to classify this variant. GT-specific criteria met: PM2_Supporting. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2048505090; hg19: chr17-42449775; API