Variant rs7168069 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001004439.2(ITGA11):c.1571T>G(p.Leu524Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 1,593,132 control chromosomes in the GnomAD database, including 560,427 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.86 ( 56025 hom., cov: 30)

Exomes 𝑓: 0.84 ( 504402 hom. )

Consequence

ITGA11
NM_001004439.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.355

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=1.1494022E-6).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ITGA11	NM_001004439.2 linkuse as main transcript	c.1571T>G	p.Leu524Arg	missense_variant	14/30	ENST00000315757.9
ITGA11	XM_011521363.3 linkuse as main transcript	c.1364T>G	p.Leu455Arg	missense_variant	12/28
ITGA11	XM_005254228.4 linkuse as main transcript	c.1265T>G	p.Leu422Arg	missense_variant	12/28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA11	ENST00000315757.9 linkuse as main transcript	c.1571T>G	p.Leu524Arg	missense_variant	14/30	1	NM_001004439.2	P4	Q9UKX5-1
ITGA11	ENST00000423218.6 linkuse as main transcript	c.1571T>G	p.Leu524Arg	missense_variant	14/30	2		A1	Q9UKX5-2
ITGA11	ENST00000566429.1 linkuse as main transcript	n.460T>G		non_coding_transcript_exon_variant	5/5	4
ITGA11	ENST00000569346.5 linkuse as main transcript	n.550T>G		non_coding_transcript_exon_variant	3/4	4

Frequencies

GnomAD3 genomes

AF:

0.858

AC:

130305

AN:

151938

Hom.:

55987

Cov.:

show subpopulations

Gnomad AFR

AF:

0.876

Gnomad AMI

AF:

0.862

Gnomad AMR

AF:

0.899

Gnomad ASJ

AF:

0.824

Gnomad EAS

AF:

0.919

Gnomad SAS

AF:

0.926

Gnomad FIN

AF:

0.874

Gnomad MID

AF:

0.858

Gnomad NFE

AF:

0.827

Gnomad OTH

AF:

0.853

GnomAD3 exomes

AF:

0.866

AC:

189692

AN:

219128

Hom.:

82335

AF XY:

0.864

AC XY:

101677

AN XY:

117620

show subpopulations

Gnomad AFR exome

AF:

0.876

Gnomad AMR exome

AF:

0.931

Gnomad ASJ exome

AF:

0.830

Gnomad EAS exome

AF:

0.917

Gnomad SAS exome

AF:

0.919

Gnomad FIN exome

AF:

0.867

Gnomad NFE exome

AF:

0.824

Gnomad OTH exome

AF:

0.856

GnomAD4 exome

AF:

0.836

AC:

1204381

AN:

1441076

Hom.:

504402

Cov.:

AF XY:

0.838

AC XY:

598659

AN XY:

714524

show subpopulations

Gnomad4 AFR exome

AF:

0.877

Gnomad4 AMR exome

AF:

0.926

Gnomad4 ASJ exome

AF:

0.830

Gnomad4 EAS exome

AF:

0.921

Gnomad4 SAS exome

AF:

0.919

Gnomad4 FIN exome

AF:

0.862

Gnomad4 NFE exome

AF:

0.820

Gnomad4 OTH exome

AF:

0.845

GnomAD4 genome

AF:

0.858

AC:

130401

AN:

152056

Hom.:

56025

Cov.:

AF XY:

0.863

AC XY:

64122

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.876

Gnomad4 AMR

AF:

0.899

Gnomad4 ASJ

AF:

0.824

Gnomad4 EAS

AF:

0.918

Gnomad4 SAS

AF:

0.925

Gnomad4 FIN

AF:

0.874

Gnomad4 NFE

AF:

0.827

Gnomad4 OTH

AF:

0.851

Alfa

AF:

0.834

Hom.:

106950

Bravo

AF:

0.860

TwinsUK

AF:

0.811

AC:

3006

ALSPAC

AF:

0.817

AC:

3148

ESP6500AA

AF:

0.894

AC:

3491

ESP6500EA

AF:

0.823

AC:

6830

ExAC

AF:

0.855

AC:

102865

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.041

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.2

DANN

Benign

0.13

DEOGEN2

Benign

0.066

.;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.0029

LIST_S2

Benign

0.022

T;T

MetaRNN

Benign

0.0000011

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.2

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.28

PROVEAN

Benign

1.3

N;N

REVEL

Benign

0.086

Sift

Benign

1.0

T;T

Sift4G

Benign

0.58

T;T

Polyphen

0.0

.;B

Vest4

0.042

MPC

0.16

ClinPred

0.00041

GERP RS

4.1

Varity_R

0.076

gMVP

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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