rs3111397

chr2-160194852-C-T

Variant summary

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

The NM_000888.5(ITGB6):c.593+517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,122 control chromosomes in the GnomAD database, including 46,498 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 0.78 (46498 hom., cov: 32)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB6	NM_000888.5	c.593+517G>A		intron_variant		ENST00000283249.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB6	ENST00000283249.7	c.593+517G>A		intron_variant		1	NM_000888.5	P1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118513 AN: 152004 Hom.: 46466 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.780 AC: 118585 AN: 152122 Hom.: 46498 Cov.: 32 AF XY: 0.780 AC XY: 57991 AN XY: 74358

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.770

Alfa AF: 0.791 Hom.: 74226

Bravo AF: 0.763

Asia WGS AF: 0.835 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.45
Dann	Benign	0.34

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: rs3111397; hg19: chr2-161051363;