2-160112327-G-T

Position:

• chr2-160112327-G-T

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.1982-128C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 786,728 control chromosomes in the GnomAD database, including 165,662 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.67 (34164 hom., cov: 30)
  • Exomes 𝑓: 0.63 (131498 hom.)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0640

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=-0.79).
• BP6: Variant 2-160112327-G-T is Benign according to our data. Variant chr2-160112327-G-T is described in ClinVar as [Benign]. Clinvar id is 1251142.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB6	NM_000888.5	c.1982-128C>A		intron_variant		ENST00000283249.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB6	ENST00000283249.7	c.1982-128C>A		intron_variant		1	NM_000888.5	P1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101201 AN: 151638 Hom.: 34126 Cov.: 30

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.632 AC: 401400 AN: 634974 Hom.: 131498 AF XY: 0.626 AC XY: 208714 AN XY: 333404

Gnomad4 AFR exome AF: 0.632

Gnomad4 AMR exome AF: 0.738

Gnomad4 ASJ exome AF: 0.556

Gnomad4 EAS exome AF: 0.502

Gnomad4 SAS exome AF: 0.478

Gnomad4 FIN exome AF: 0.684

Gnomad4 NFE exome AF: 0.655

Gnomad4 OTH exome AF: 0.635

GnomAD4 genome AF: 0.668 AC: 101299 AN: 151754 Hom.: 34164 Cov.: 30 AF XY: 0.667 AC XY: 49460 AN XY: 74148

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.639

Alfa AF: 0.677 Hom.: 4343

Bravo AF: 0.674

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.62

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: rs11895959; hg19: chr2-160968838;