Variant rs2269772 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_002204.4(ITGA3):c.996C>T(p.Phe332=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,613,448 control chromosomes in the GnomAD database, including 16,649 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3528 hom., cov: 31)

Exomes 𝑓: 0.11 ( 13121 hom. )

Consequence

ITGA3
NM_002204.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.999

Variant links:

Genes affected

ITGA3 (HGNC:6139): (integrin subunit alpha 3) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function as cell surface adhesion molecules. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 3 subunit. This subunit joins with a beta 1 subunit to form an integrin that interacts with extracellular matrix proteins including members of the laminin family. Expression of this gene may be correlated with breast cancer metastasis. [provided by RefSeq, Oct 2015]

ITGA3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 17-50072022-C-T is Benign according to our data. Variant chr17-50072022-C-T is described in ClinVar as [Benign]. Clinvar id is 1271410.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.999 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ITGA3	NM_002204.4 linkuse as main transcript	c.996C>T	p.Phe332=	synonymous_variant	7/26	ENST00000320031.13
ITGA3	XM_047435922.1 linkuse as main transcript	c.996C>T	p.Phe332=	synonymous_variant	7/18
ITGA3	XM_005257308.3 linkuse as main transcript	c.751+1092C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA3	ENST00000320031.13 linkuse as main transcript	c.996C>T	p.Phe332=	synonymous_variant	7/26	1	NM_002204.4	P1	P26006-2

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28077

AN:

151844

Hom.:

3511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.0813

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.0975

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0889

Gnomad OTH

AF:

0.165

GnomAD3 exomes

AF:

0.167

AC:

41908

AN:

250798

Hom.:

4639

AF XY:

0.162

AC XY:

21919

AN XY:

135622

show subpopulations

Gnomad AFR exome

AF:

0.344

Gnomad AMR exome

AF:

0.250

Gnomad ASJ exome

AF:

0.113

Gnomad EAS exome

AF:

0.320

Gnomad SAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.0991

Gnomad NFE exome

AF:

0.0927

Gnomad OTH exome

AF:

0.141

GnomAD4 exome

AF:

0.114

AC:

166596

AN:

1461486

Hom.:

13121

Cov.:

AF XY:

0.116

AC XY:

84575

AN XY:

727078

show subpopulations

Gnomad4 AFR exome

AF:

0.342

Gnomad4 AMR exome

AF:

0.246

Gnomad4 ASJ exome

AF:

0.115

Gnomad4 EAS exome

AF:

0.316

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.0970

Gnomad4 NFE exome

AF:

0.0850

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.185

AC:

28157

AN:

151962

Hom.:

3528

Cov.:

AF XY:

0.189

AC XY:

14048

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.337

Gnomad4 AMR

AF:

0.224

Gnomad4 ASJ

AF:

0.118

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.254

Gnomad4 FIN

AF:

0.0975

Gnomad4 NFE

AF:

0.0889

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.118

Hom.:

1935

Bravo

AF:

0.199

Asia WGS

AF:

0.292

AC:

1016

AN:

3478

EpiCase

AF:

0.0936

EpiControl

AF:

0.0961

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	Invitae	Jan 31, 2024	- -
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

-0.46

CADD

Benign

8.8

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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