Variant 17-50073989-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002204.4(ITGA3):c.1230T>C(p.Leu410=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,612,682 control chromosomes in the GnomAD database, including 26,897 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 5698 hom., cov: 32)

Exomes 𝑓: 0.15 ( 21199 hom. )

Consequence

ITGA3
NM_002204.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.91

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 -21 ACMG points.

BP4

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

BP6

Variant 17-50073989-T-C is Benign according to our data. Variant chr17-50073989-T-C is described in ClinVar as [Benign]. Clinvar id is 1271172.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ITGA3	NM_002204.4 linkuse as main transcript	c.1230T>C	p.Leu410=	synonymous_variant	8/26	ENST00000320031.13
ITGA3	XM_005257308.3 linkuse as main transcript	c.825T>C	p.Leu275=	synonymous_variant	6/24
ITGA3	XM_047435922.1 linkuse as main transcript	c.1230T>C	p.Leu410=	synonymous_variant	8/18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA3	ENST00000320031.13 linkuse as main transcript	c.1230T>C	p.Leu410=	synonymous_variant	8/26	1	NM_002204.4	P1	P26006-2

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36133

AN:

151936

Hom.:

5668

Cov.:

show subpopulations

Gnomad AFR

AF:

0.420

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.217

GnomAD3 exomes

AF:

0.214

AC:

53173

AN:

248882

Hom.:

7385

AF XY:

0.204

AC XY:

27531

AN XY:

134736

show subpopulations

Gnomad AFR exome

AF:

0.426

Gnomad AMR exome

AF:

0.364

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.341

Gnomad SAS exome

AF:

0.277

Gnomad FIN exome

AF:

0.137

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.179

GnomAD4 exome

AF:

0.149

AC:

217757

AN:

1460628

Hom.:

21199

Cov.:

AF XY:

0.151

AC XY:

109856

AN XY:

726700

show subpopulations

Gnomad4 AFR exome

AF:

0.427

Gnomad4 AMR exome

AF:

0.358

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.340

Gnomad4 SAS exome

AF:

0.275

Gnomad4 FIN exome

AF:

0.137

Gnomad4 NFE exome

AF:

0.116

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.238

AC:

36234

AN:

152054

Hom.:

5698

Cov.:

AF XY:

0.243

AC XY:

18035

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.421

Gnomad4 AMR

AF:

0.317

Gnomad4 ASJ

AF:

0.130

Gnomad4 EAS

AF:

0.344

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.222

Alfa

AF:

0.166

Hom.:

2073

Bravo

AF:

0.257

Asia WGS

AF:

0.339

AC:

1178

AN:

3478

EpiCase

AF:

0.123

EpiControl

AF:

0.124

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
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

2.7

DANN

Benign

0.52

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