Variant rs2303126 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.2235+72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 1,488,422 control chromosomes in the GnomAD database, including 6,298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.074 ( 588 hom., cov: 33)

Exomes 𝑓: 0.083 ( 5710 hom. )

Consequence

ITGA2
NM_002203.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0960

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 5-53070332-G-A is Benign according to our data. Variant chr5-53070332-G-A is described in ClinVar as [Benign]. Clinvar id is 1255354.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 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.2235+72G>A		intron_variant		ENST00000296585.10	NP_002194.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA2	ENST00000296585.10 linkuse as main transcript	c.2235+72G>A		intron_variant		1	NM_002203.4	ENSP00000296585	P1

Frequencies

GnomAD3 genomes

AF:

0.0741

AC:

11248

AN:

151724

Hom.:

586

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0299

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.172

Gnomad SAS

AF:

0.0982

Gnomad FIN

AF:

0.0851

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0701

Gnomad OTH

AF:

0.0762

GnomAD4 exome

AF:

0.0827

AC:

110584

AN:

1336580

Hom.:

5710

AF XY:

0.0822

AC XY:

55183

AN XY:

671502

show subpopulations

Gnomad4 AFR exome

AF:

0.0280

Gnomad4 AMR exome

AF:

0.217

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.0877

Gnomad4 FIN exome

AF:

0.0867

Gnomad4 NFE exome

AF:

0.0720

Gnomad4 OTH exome

AF:

0.0874

GnomAD4 genome

AF:

0.0741

AC:

11254

AN:

151842

Hom.:

588

Cov.:

AF XY:

0.0760

AC XY:

5640

AN XY:

74180

show subpopulations

Gnomad4 AFR

AF:

0.0298

Gnomad4 AMR

AF:

0.161

Gnomad4 ASJ

AF:

0.100

Gnomad4 EAS

AF:

0.172

Gnomad4 SAS

AF:

0.0983

Gnomad4 FIN

AF:

0.0851

Gnomad4 NFE

AF:

0.0701

Gnomad4 OTH

AF:

0.0802

Alfa

AF:

0.0673

Hom.:

Bravo

AF:

0.0797

Asia WGS

AF:

0.143

AC:

497

AN:

3476

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.4

DANN

Benign

0.45

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

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