rs2925757

Variant names:

• chr2-160244658-G-A
• rs2925757
• ENST00000485635.1:n.169+27062C>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000485635.1(ENSG00000285155):​n.169+27062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,148 control chromosomes in the GnomAD database, including 53,845 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 0.84 (53845 hom., cov: 31)
• Consequence: ENSG00000285155 ENST00000485635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 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.169+27062C>T		intron_variant	Intron 1 of 9	2		ENSP00000520446.1
ENSG00000285155	ENST00000498478.1	n.260+8932C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127731 AN: 152030 Hom.: 53790 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.840 AC: 127839 AN: 152148 Hom.: 53845 Cov.: 31 AF XY: 0.841 AC XY: 62588 AN XY: 74380

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.825

Alfa AF: 0.832 Hom.: 14695

Bravo AF: 0.844

Asia WGS AF: 0.863 AC: 2997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925757; hg19: chr2-161101169;