Variant chr2-160112117-A-G 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_000888.5(ITGB6):c.2064T>C(p.Asn688=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,611,606 control chromosomes in the GnomAD database, including 29,401 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3218 hom., cov: 31)

Exomes 𝑓: 0.18 ( 26183 hom. )

Consequence

ITGB6
NM_000888.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.13

Variant links:

Genes affected

ITGB6 (HGNC:6161): (integrin subunit beta 6) This gene encodes a protein that is a member of the integrin superfamily. Members of this family are adhesion receptors that function in signaling from the extracellular matrix to the cell. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. The encoded protein forms a dimer with an alpha v chain and this heterodimer can bind to ligands like fibronectin and transforming growth factor beta 1. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ITGB6 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=-0.63).

BP6

Variant 2-160112117-A-G is Benign according to our data. Variant chr2-160112117-A-G is described in ClinVar as [Benign]. Clinvar id is 1227008.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.13 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB6	NM_000888.5 linkuse as main transcript	c.2064T>C	p.Asn688=	synonymous_variant	13/15	ENST00000283249.7	NP_000879.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB6	ENST00000283249.7 linkuse as main transcript	c.2064T>C	p.Asn688=	synonymous_variant	13/15	1	NM_000888.5	ENSP00000283249	P1	P18564-1

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29742

AN:

151948

Hom.:

3198

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.202

GnomAD3 exomes

AF:

0.204

AC:

51057

AN:

250254

Hom.:

6542

AF XY:

0.190

AC XY:

25729

AN XY:

135180

show subpopulations

Gnomad AFR exome

AF:

0.210

Gnomad AMR exome

AF:

0.440

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.170

Gnomad SAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.165

Gnomad NFE exome

AF:

0.169

Gnomad OTH exome

AF:

0.203

GnomAD4 exome

AF:

0.181

AC:

264588

AN:

1459542

Hom.:

26183

Cov.:

AF XY:

0.178

AC XY:

129185

AN XY:

726090

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.158

Gnomad4 EAS exome

AF:

0.165

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.164

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.183

GnomAD4 genome

AF:

0.196

AC:

29792

AN:

152064

Hom.:

3218

Cov.:

AF XY:

0.196

AC XY:

14536

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.166

Gnomad4 SAS

AF:

0.138

Gnomad4 FIN

AF:

0.160

Gnomad4 NFE

AF:

0.172

Gnomad4 OTH

AF:

0.201

Alfa

AF:

0.173

Hom.:

5308

Bravo

AF:

0.212

Asia WGS

AF:

0.161

AC:

564

AN:

3478

EpiCase

AF:

0.171

EpiControl

AF:

0.172

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.37

DANN

Benign

0.61

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