Variant rs11870252 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 ENST00000559488.7(ITGB3):c.1914-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 1,594,948 control chromosomes in the GnomAD database, including 5,629 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 606 hom., cov: 32)

Exomes 𝑓: 0.077 ( 5023 hom. )

Consequence

ITGB3
ENST00000559488.7 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.383

Variant links:

Genes affected

ITGB3 (HGNC:6156): (integrin subunit beta 3) The ITGB3 protein product is the integrin beta chain beta 3. Integrins are integral cell-surface proteins composed of an alpha chain and a beta chain. A given chain may combine with multiple partners resulting in different integrins. Integrin beta 3 is found along with the alpha IIb chain in platelets. Integrins are known to participate in cell adhesion as well as cell-surface mediated signalling. [provided by RefSeq, Jul 2008]

ITGB3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 17-47300459-T-C is Benign according to our data. Variant chr17-47300459-T-C is described in ClinVar as [Benign]. Clinvar id is 255538.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB3	NM_000212.3 linkuse as main transcript	c.1914-19T>C		intron_variant		ENST00000559488.7	NP_000203.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7 linkuse as main transcript	c.1914-19T>C		intron_variant		1	NM_000212.3	ENSP00000452786	P1	P05106-1
ITGB3	ENST00000696963.1 linkuse as main transcript	c.1914-19T>C		intron_variant				ENSP00000513002		P05106-2

Frequencies

GnomAD3 genomes

AF:

0.0858

AC:

13044

AN:

152098

Hom.:

605

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0968

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.0833

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.0350

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.0723

Gnomad OTH

AF:

0.0985

GnomAD3 exomes

AF:

0.0885

AC:

22219

AN:

251082

Hom.:

1173

AF XY:

0.0909

AC XY:

12336

AN XY:

135722

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.0552

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.192

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0392

Gnomad NFE exome

AF:

0.0759

Gnomad OTH exome

AF:

0.0982

GnomAD4 exome

AF:

0.0766

AC:

110569

AN:

1442732

Hom.:

5023

Cov.:

AF XY:

0.0782

AC XY:

56235

AN XY:

718980

show subpopulations

Gnomad4 AFR exome

AF:

0.0931

Gnomad4 AMR exome

AF:

0.0595

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.186

Gnomad4 SAS exome

AF:

0.120

Gnomad4 FIN exome

AF:

0.0416

Gnomad4 NFE exome

AF:

0.0685

Gnomad4 OTH exome

AF:

0.0888

GnomAD4 genome

AF:

0.0858

AC:

13055

AN:

152216

Hom.:

606

Cov.:

AF XY:

0.0852

AC XY:

6343

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0967

Gnomad4 AMR

AF:

0.0832

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.192

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.0350

Gnomad4 NFE

AF:

0.0724

Gnomad4 OTH

AF:

0.0970

Alfa

AF:

0.0831

Hom.:

111

Bravo

AF:

0.0910

Asia WGS

AF:

0.138

AC:

481

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.039

DANN

Benign

0.27

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