Variant 3-37494565-C-T 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_002207.3(ITGA9):c.609C>T(p.Thr203=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 1,611,664 control chromosomes in the GnomAD database, including 2,732 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 205 hom., cov: 33)

Exomes 𝑓: 0.056 ( 2527 hom. )

Consequence

ITGA9
NM_002207.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.91

Variant links:

Genes affected

ITGA9 (HGNC:6145): (integrin subunit alpha 9) This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane glycoproteins composed of an alpha chain and a beta chain that mediate cell-cell and cell-matrix adhesion. The protein encoded by this gene, when bound to the beta 1 chain, forms an integrin that is a receptor for VCAM1, cytotactin and osteopontin. Expression of this gene has been found to be upregulated in small cell lung cancers. [provided by RefSeq, Jul 2008]

ITGA9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 3-37494565-C-T is Benign according to our data. Variant chr3-37494565-C-T is described in ClinVar as [Benign]. Clinvar id is 402988.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-37494565-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA9	NM_002207.3 linkuse as main transcript	c.609C>T	p.Thr203=	synonymous_variant	5/28	ENST00000264741.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA9	ENST00000264741.10 linkuse as main transcript	c.609C>T	p.Thr203=	synonymous_variant	5/28	1	NM_002207.3	P1
ITGA9	ENST00000422441.5 linkuse as main transcript	c.609C>T	p.Thr203=	synonymous_variant	5/16	1

Frequencies

GnomAD3 genomes

AF:

0.0455

AC:

6922

AN:

152172

Hom.:

206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0149

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0701

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.0706

Gnomad SAS

AF:

0.0466

Gnomad FIN

AF:

0.0257

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0590

Gnomad OTH

AF:

0.0573

GnomAD3 exomes

AF:

0.0491

AC:

12312

AN:

250738

Hom.:

328

AF XY:

0.0504

AC XY:

6826

AN XY:

135568

show subpopulations

Gnomad AFR exome

AF:

0.0147

Gnomad AMR exome

AF:

0.0470

Gnomad ASJ exome

AF:

0.0369

Gnomad EAS exome

AF:

0.0641

Gnomad SAS exome

AF:

0.0508

Gnomad FIN exome

AF:

0.0259

Gnomad NFE exome

AF:

0.0569

Gnomad OTH exome

AF:

0.0557

GnomAD4 exome

AF:

0.0560

AC:

81797

AN:

1459374

Hom.:

2527

Cov.:

AF XY:

0.0557

AC XY:

40454

AN XY:

726126

show subpopulations

Gnomad4 AFR exome

AF:

0.0135

Gnomad4 AMR exome

AF:

0.0490

Gnomad4 ASJ exome

AF:

0.0374

Gnomad4 EAS exome

AF:

0.0731

Gnomad4 SAS exome

AF:

0.0522

Gnomad4 FIN exome

AF:

0.0265

Gnomad4 NFE exome

AF:

0.0589

Gnomad4 OTH exome

AF:

0.0596

GnomAD4 genome

AF:

0.0455

AC:

6926

AN:

152290

Hom.:

205

Cov.:

AF XY:

0.0454

AC XY:

3382

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0149

Gnomad4 AMR

AF:

0.0699

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.0706

Gnomad4 SAS

AF:

0.0466

Gnomad4 FIN

AF:

0.0257

Gnomad4 NFE

AF:

0.0590

Gnomad4 OTH

AF:

0.0605

Alfa

AF:

0.0559

Hom.:

472

Bravo

AF:

0.0476

Asia WGS

AF:

0.0550

AC:

189

AN:

3478

EpiCase

AF:

0.0587

EpiControl

AF:

0.0637

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 5% of total chromosomes in ExAC -

not provided

Benign:1

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

-0.57

CADD

Benign

5.5

DANN

Benign

0.66

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