rs10497211

Positions:

• chr2-160125285-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000888.5(ITGB6):​c.1883+1094G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0661 in 152,292 control chromosomes in the GnomAD database, including 379 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.066 (379 hom., cov: 33)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB6	NM_000888.5	c.1883+1094G>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.1883+1094G>C		intron_variant		1	NM_000888.5	ENSP00000283249.2

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10060 AN: 152174 Hom.: 379 Cov.: 33

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0661 AC: 10061 AN: 152292 Hom.: 379 Cov.: 33 AF XY: 0.0648 AC XY: 4826 AN XY: 74474

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.0348

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.0786

Alfa AF: 0.0696 Hom.: 50

Bravo AF: 0.0683

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.22
DANN	Benign	0.37

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: rs10497211; hg19: chr2-160981796;