2-160112232-CA-C

Position:

• chr2-160112232-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000888.5(ITGB6):​c.1982-34del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.59 (27970 hom., cov: 0)
  • Exomes 𝑓: 0.66 (313686 hom.)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.369

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 -10 ACMG points.

• BP6: Variant 2-160112232-CA-C is Benign according to our data. Variant chr2-160112232-CA-C is described in ClinVar as [Benign]. Clinvar id is 1238798.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB6	NM_000888.5	c.1982-34del		intron_variant		ENST00000283249.7	NP_000879.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB6	ENST00000283249.7	c.1982-34del		intron_variant		1	NM_000888.5	ENSP00000283249	P1

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89997 AN: 151830 Hom.: 27950 Cov.: 0

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.583

GnomAD3 exomes AF: 0.626 AC: 147974 AN: 236386 Hom.: 48027 AF XY: 0.620 AC XY: 79312 AN XY: 127832

Gnomad AFR exome AF: 0.403

Gnomad AMR exome AF: 0.759

Gnomad ASJ exome AF: 0.507

Gnomad EAS exome AF: 0.460

Gnomad SAS exome AF: 0.491

Gnomad FIN exome AF: 0.687

Gnomad NFE exome AF: 0.679

Gnomad OTH exome AF: 0.649

GnomAD4 exome AF: 0.657 AC: 937611 AN: 1426244 Hom.: 313686 Cov.: 0 AF XY: 0.652 AC XY: 463538 AN XY: 710618

Gnomad4 AFR exome AF: 0.390

Gnomad4 AMR exome AF: 0.749

Gnomad4 ASJ exome AF: 0.515

Gnomad4 EAS exome AF: 0.504

Gnomad4 SAS exome AF: 0.492

Gnomad4 FIN exome AF: 0.687

Gnomad4 NFE exome AF: 0.684

Gnomad4 OTH exome AF: 0.633

GnomAD4 genome AF: 0.593 AC: 90058 AN: 151946 Hom.: 27970 Cov.: 0 AF XY: 0.596 AC XY: 44253 AN XY: 74278

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.582

Alfa AF: 0.623 Hom.: 5471

Bravo AF: 0.586

Asia WGS AF: 0.531 AC: 1847 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

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: rs66470452; hg19: chr2-160968743;