Variant rs984966 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002203.4(ITGA2):c.2430-26T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 1,604,542 control chromosomes in the GnomAD database, including 125,230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10329 hom., cov: 31)

Exomes 𝑓: 0.39 ( 114901 hom. )

Consequence

ITGA2
NM_002203.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0720

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:

ITGA2 (HGNC:):

ITGA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 5-53073092-T-A is Benign according to our data. Variant chr5-53073092-T-A is described in ClinVar as [Benign]. Clinvar id is 1226263.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA2	NM_002203.4 linkuse as main transcript	c.2430-26T>A		intron_variant		ENST00000296585.10	NP_002194.2	P17301

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA2	ENST00000296585.10 linkuse as main transcript	c.2430-26T>A		intron_variant		1	NM_002203.4	ENSP00000296585.5		P17301

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55555

AN:

151550

Hom.:

10330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.290

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.376

GnomAD3 exomes

AF:

0.387

AC:

96541

AN:

249334

Hom.:

18994

AF XY:

0.386

AC XY:

52136

AN XY:

134894

show subpopulations

Gnomad AFR exome

AF:

0.290

Gnomad AMR exome

AF:

0.457

Gnomad ASJ exome

AF:

0.386

Gnomad EAS exome

AF:

0.299

Gnomad SAS exome

AF:

0.363

Gnomad FIN exome

AF:

0.398

Gnomad NFE exome

AF:

0.399

Gnomad OTH exome

AF:

0.386

GnomAD4 exome

AF:

0.395

AC:

573752

AN:

1452872

Hom.:

114901

Cov.:

AF XY:

0.394

AC XY:

285031

AN XY:

723180

show subpopulations

Gnomad4 AFR exome

AF:

0.288

Gnomad4 AMR exome

AF:

0.454

Gnomad4 ASJ exome

AF:

0.389

Gnomad4 EAS exome

AF:

0.360

Gnomad4 SAS exome

AF:

0.366

Gnomad4 FIN exome

AF:

0.398

Gnomad4 NFE exome

AF:

0.400

Gnomad4 OTH exome

AF:

0.388

GnomAD4 genome

AF:

0.366

AC:

55573

AN:

151670

Hom.:

10329

Cov.:

AF XY:

0.367

AC XY:

27188

AN XY:

74082

show subpopulations

Gnomad4 AFR

AF:

0.290

Gnomad4 AMR

AF:

0.427

Gnomad4 ASJ

AF:

0.370

Gnomad4 EAS

AF:

0.306

Gnomad4 SAS

AF:

0.352

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.399

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.317

Hom.:

1462

Bravo

AF:

0.367

Asia WGS

AF:

0.333

AC:

1157

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.12

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

Details are displayed if max score is > 0.2

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