chr2-160130410-G-T

Position:

• chr2-160130410-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.1661-3809C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,822 control chromosomes in the GnomAD database, including 34,337 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 0.67 (34337 hom., cov: 31)
• Consequence: ITGB6 NM_000888.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB6	NM_000888.5	c.1661-3809C>A		intron_variant		ENST00000283249.7	NP_000879.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB6	ENST00000283249.7	c.1661-3809C>A		intron_variant		1	NM_000888.5	ENSP00000283249.2

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101481 AN: 151706 Hom.: 34298 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.669 AC: 101578 AN: 151822 Hom.: 34337 Cov.: 31 AF XY: 0.669 AC XY: 49615 AN XY: 74174

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.641

Alfa AF: 0.579 Hom.: 1634

Bravo AF: 0.674

Asia WGS AF: 0.546 AC: 1890 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.79

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: rs10497208; hg19: chr2-160986921;