Variant 15-68335825-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000315757.9(ITGA11):c.1297G>A(p.Val433Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 1,612,980 control chromosomes in the GnomAD database, including 5,339 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.058 ( 339 hom., cov: 33)

Exomes 𝑓: 0.080 ( 5000 hom. )

Consequence

ITGA11
ENST00000315757.9 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Variant links:

Genes affected

ITGA11 (HGNC:6136): (integrin subunit alpha 11) This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein contains an I domain, is expressed in muscle tissue, dimerizes with beta 1 integrin in vitro, and appears to bind collagen in this form. Therefore, the protein may be involved in attaching muscle tissue to the extracellular matrix. Alternative transcriptional splice variants have been found for this gene, but their biological validity is not determined. [provided by RefSeq, Jul 2008]

ITGA11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008588225).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ITGA11	NM_001004439.2 linkuse as main transcript	c.1297G>A	p.Val433Met	missense_variant	12/30	ENST00000315757.9	NP_001004439.1
ITGA11	XM_011521363.3 linkuse as main transcript	c.1090G>A	p.Val364Met	missense_variant	10/28		XP_011519665.1
ITGA11	XM_005254228.4 linkuse as main transcript	c.991G>A	p.Val331Met	missense_variant	10/28		XP_005254285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA11	ENST00000315757.9 linkuse as main transcript	c.1297G>A	p.Val433Met	missense_variant	12/30	1	NM_001004439.2	ENSP00000327290	P4	Q9UKX5-1
ITGA11	ENST00000423218.6 linkuse as main transcript	c.1297G>A	p.Val433Met	missense_variant	12/30	2		ENSP00000403392	A1	Q9UKX5-2
ITGA11	ENST00000569346.5 linkuse as main transcript	n.276G>A		non_coding_transcript_exon_variant	1/4	4
ITGA11	ENST00000566429.1 linkuse as main transcript	n.197-11G>A		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0583

AC:

8881

AN:

152212

Hom.:

339

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0333

Gnomad ASJ

AF:

0.0530

Gnomad EAS

AF:

0.0793

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.0774

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0858

Gnomad OTH

AF:

0.0616

GnomAD3 exomes

AF:

0.0664

AC:

16351

AN:

246158

Hom.:

683

AF XY:

0.0679

AC XY:

9089

AN XY:

133850

show subpopulations

Gnomad AFR exome

AF:

0.0145

Gnomad AMR exome

AF:

0.0212

Gnomad ASJ exome

AF:

0.0592

Gnomad EAS exome

AF:

0.0779

Gnomad SAS exome

AF:

0.0550

Gnomad FIN exome

AF:

0.0855

Gnomad NFE exome

AF:

0.0857

Gnomad OTH exome

AF:

0.0659

GnomAD4 exome

AF:

0.0803

AC:

117314

AN:

1460650

Hom.:

5000

Cov.:

AF XY:

0.0796

AC XY:

57841

AN XY:

726526

show subpopulations

Gnomad4 AFR exome

AF:

0.0128

Gnomad4 AMR exome

AF:

0.0232

Gnomad4 ASJ exome

AF:

0.0569

Gnomad4 EAS exome

AF:

0.0787

Gnomad4 SAS exome

AF:

0.0548

Gnomad4 FIN exome

AF:

0.0855

Gnomad4 NFE exome

AF:

0.0877

Gnomad4 OTH exome

AF:

0.0707

GnomAD4 genome

AF:

0.0584

AC:

8889

AN:

152330

Hom.:

339

Cov.:

AF XY:

0.0571

AC XY:

4252

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.0155

Gnomad4 AMR

AF:

0.0332

Gnomad4 ASJ

AF:

0.0530

Gnomad4 EAS

AF:

0.0794

Gnomad4 SAS

AF:

0.0547

Gnomad4 FIN

AF:

0.0774

Gnomad4 NFE

AF:

0.0858

Gnomad4 OTH

AF:

0.0643

Alfa

AF:

0.0779

Hom.:

1279

Bravo

AF:

0.0524

TwinsUK

AF:

0.0976

AC:

362

ALSPAC

AF:

0.0885

AC:

341

ESP6500AA

AF:

0.0157

AC:

ESP6500EA

AF:

0.0822

AC:

693

ExAC

AF:

0.0663

AC:

8024

Asia WGS

AF:

0.0820

AC:

283

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.14

.;T

Eigen

Benign

-0.23

Eigen_PC

Benign

-0.18

FATHMM_MKL

Benign

0.10

LIST_S2

Benign

0.84

T;T

MetaRNN

Benign

0.0086

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.1

L;L

MutationTaster

Benign

0.0043

P;P

PrimateAI

Uncertain

0.48

PROVEAN

Benign

-0.86

N;N

REVEL

Benign

0.12

Sift

Benign

0.074

T;T

Sift4G

Benign

0.070

T;T

Polyphen

0.93

.;P

Vest4

0.045

MPC

0.12

ClinPred

0.027

GERP RS

3.5

Varity_R

0.047

gMVP

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over