chr2-160203673-A-G

Position:

• chr2-160203673-A-G

Variant summary

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

The variant allele was found at a frequency of 0.304 in 152,120 control chromosomes in the GnomAD database, including 8,739 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 0.30 (8739 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

(HGNC:):

ENSG00000285155 (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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.160203673A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285155	ENST00000485635.1	n.380+2190T>C		intron_variant		2		ENSP00000520446.1
ENSG00000285155	ENST00000498478.1	n.261-2456T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46246 AN: 152002 Hom.: 8738 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.304 AC: 46251 AN: 152120 Hom.: 8739 Cov.: 32 AF XY: 0.307 AC XY: 22812 AN XY: 74344

Gnomad4 AFR AF: 0.0908

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.286

Alfa AF: 0.359 Hom.: 1378

Bravo AF: 0.281

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4665162; hg19: chr2-161060184;