Variant rs57674800 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002203.4(ITGA2):c.*3599_*3600insTATATAAACAACTTTGTAGGACTAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.35 ( 9517 hom., cov: 0)

Exomes 𝑓: 0.50 ( 3 hom. )

Consequence

ITGA2
NM_002203.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.877

Variant links:

Genes affected

ITGA2 (HGNC:6137): (integrin subunit alpha 2) This gene encodes the alpha subunit of a transmembrane receptor for collagens and related proteins. The encoded protein forms a heterodimer with a beta subunit and mediates the adhesion of platelets and other cell types to the extracellular matrix. Loss of the encoded protein is associated with bleeding disorder platelet-type 9. Antibodies against this protein are found in several immune disorders, including neonatal alloimmune thrombocytopenia. This gene is located adjacent to a related alpha subunit gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ITGA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2	NM_002203.4 linkuse as main transcript	c.3599_3600insTATATAAACAACTTTGTAGGACTAT		3_prime_UTR_variant	30/30	ENST00000296585.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2	ENST00000296585.10 linkuse as main transcript	c.3599_3600insTATATAAACAACTTTGTAGGACTAT		3_prime_UTR_variant	30/30	1	NM_002203.4	P1

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53460

AN:

151866

Hom.:

9513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.401

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.374

Gnomad OTH

AF:

0.357

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.550

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.352

AC:

53478

AN:

151978

Hom.:

9517

Cov.:

AF XY:

0.354

AC XY:

26294

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.286

Gnomad4 AMR

AF:

0.411

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.313

Gnomad4 SAS

AF:

0.347

Gnomad4 FIN

AF:

0.401

Gnomad4 NFE

AF:

0.374

Gnomad4 OTH

AF:

0.358

Alfa

AF:

0.221

Hom.:

341

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Platelet-type bleeding disorder 9

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over