chr2-160111767-A-G

Position:

• chr2-160111767-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000888.5(ITGB6):​c.2101+313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 151,972 control chromosomes in the GnomAD database, including 371 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.065 (371 hom., cov: 29)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.757

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 2-160111767-A-G is Benign according to our data. Variant chr2-160111767-A-G is described in ClinVar as [Benign]. Clinvar id is 1276734.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB6	NM_000888.5	c.2101+313T>C		intron_variant		ENST00000283249.7	NP_000879.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB6	ENST00000283249.7	c.2101+313T>C		intron_variant		1	NM_000888.5	ENSP00000283249	P1

Frequencies

GnomAD3 genomes AF: 0.0653 AC: 9919 AN: 151854 Hom.: 371 Cov.: 29

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0783

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0653 AC: 9920 AN: 151972 Hom.: 371 Cov.: 29 AF XY: 0.0640 AC XY: 4755 AN XY: 74256

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0677

Gnomad4 FIN AF: 0.0343

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.0775

Alfa AF: 0.0269 Hom.: 13

Bravo AF: 0.0676

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs12987481; hg19: chr2-160968278;