rs10181181

Variant names:

• chr2-160230900-T-C
• rs10181181
• ENST00000485635.1:n.170-24827A>G

Variant summary

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

The ENST00000485635.1(ENSG00000285155):​n.170-24827A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,120 control chromosomes in the GnomAD database, including 38,375 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 0.71 (38375 hom., cov: 32)
• Consequence: ENSG00000285155 ENST00000485635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

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]

ENSG00000285155 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285155	ENST00000485635.1	n.170-24827A>G		intron_variant	Intron 1 of 9	2		ENSP00000520446.1
ENSG00000285155	ENST00000498478.1	n.260+22690A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107402 AN: 152002 Hom.: 38331 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.707 AC: 107500 AN: 152120 Hom.: 38375 Cov.: 32 AF XY: 0.711 AC XY: 52860 AN XY: 74360

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.694

Alfa AF: 0.692 Hom.: 3700

Bravo AF: 0.705

Asia WGS AF: 0.756 AC: 2625 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	0.99
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10181181; hg19: chr2-161087411;