rs6432593

Positions:

• chr2-160108635-G-A
• chr2-160108635-G-T

Variant summary

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

The NM_000888.5(ITGB6):​c.2102-790C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,154 control chromosomes in the GnomAD database, including 48,289 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 0.79 (48289 hom., cov: 31)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB6	NM_000888.5	c.2102-790C>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.2102-790C>T		intron_variant		1	NM_000888.5	ENSP00000283249	P1

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119890 AN: 152036 Hom.: 48230 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.789 AC: 120013 AN: 152154 Hom.: 48289 Cov.: 31 AF XY: 0.790 AC XY: 58722 AN XY: 74360

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.740

Alfa AF: 0.721 Hom.: 80532

Bravo AF: 0.804

Asia WGS AF: 0.742 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.49

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: rs6432593; hg19: chr2-160965146;