chr2-160107946-G-A

Position:

• chr2-160107946-G-A

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.2102-101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0731 in 1,012,468 control chromosomes in the GnomAD database, including 3,085 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.066 (381 hom., cov: 32)
  • Exomes 𝑓: 0.074 (2704 hom.)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0950

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=-0.83).
• BP6: Variant 2-160107946-G-A is Benign according to our data. Variant chr2-160107946-G-A is described in ClinVar as [Benign]. Clinvar id is 1225831.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) 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.2102-101C>T		intron_variant		ENST00000283249.7	NP_000879.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB6	ENST00000283249.7	c.2102-101C>T		intron_variant		1	NM_000888.5	ENSP00000283249	P1

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 10036 AN: 152042 Hom.: 381 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0789

GnomAD4 exome AF: 0.0743 AC: 63949 AN: 860308 Hom.: 2704 AF XY: 0.0745 AC XY: 32187 AN XY: 432278

Gnomad4 AFR exome AF: 0.0465

Gnomad4 AMR exome AF: 0.0531

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.000392

Gnomad4 SAS exome AF: 0.0751

Gnomad4 FIN exome AF: 0.0419

Gnomad4 NFE exome AF: 0.0796

Gnomad4 OTH exome AF: 0.0784

GnomAD4 genome AF: 0.0660 AC: 10039 AN: 152160 Hom.: 381 Cov.: 32 AF XY: 0.0647 AC XY: 4813 AN XY: 74406

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0802

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0675

Gnomad4 FIN AF: 0.0348

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0695 Hom.: 51

Bravo AF: 0.0684

Asia WGS AF: 0.0460 AC: 159 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	-0.83
CADD	Benign	2.0
DANN	Benign	0.41

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: rs13010138; hg19: chr2-160964457;