rs6721348

Variant names:

• chr2-172253781-G-A
• rs6721348
• ENST00000715295.1:c.-536+19524G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-172253781-G-A
• chr2-172253781-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715295.1(ITGA6):​c.-536+19524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 151,972 control chromosomes in the GnomAD database, including 58,636 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 0.88 (58636 hom., cov: 28)
• Consequence: ITGA6 ENST00000715295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 2 publications found

Genes affected

ITGA6 (HGNC:6142): (integrin subunit alpha 6) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function in cell surface adhesion and signaling. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 6 subunit. This subunit may associate with a beta 1 or beta 4 subunit to form an integrin that interacts with extracellular matrix proteins including members of the laminin family. The alpha 6 beta 4 integrin may promote tumorigenesis, while the alpha 6 beta 1 integrin may negatively regulate erbB2/HER2 signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

DLX2-DT (HGNC:50638): (DLX2 divergent transcript)

ENSG00000295985 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985960	XR_001739773.3	n.2208+1148G>A		intron_variant	Intron 1 of 5
LOC107985960	XR_001739775.3	n.2208+1148G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA6	ENST00000715295.1	c.-536+19524G>A		intron_variant	Intron 1 of 27			ENSP00000520448.1
DLX2-DT	ENST00000662340.1	n.213-44416G>A		intron_variant	Intron 2 of 3
DLX2-DT	ENST00000667725.1	n.242-44416G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133185 AN: 151854 Hom.: 58613 Cov.: 28

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.877 AC: 133255 AN: 151972 Hom.: 58636 Cov.: 28 AF XY: 0.879 AC XY: 65339 AN XY: 74298

African (AFR) AF: 0.802 AC: 33183 AN: 41398

American (AMR) AF: 0.900 AC: 13762 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3179 AN: 3472

East Asian (EAS) AF: 0.882 AC: 4524 AN: 5132

South Asian (SAS) AF: 0.846 AC: 4040 AN: 4778

European-Finnish (FIN) AF: 0.920 AC: 9756 AN: 10604

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61841 AN: 67984

Other (OTH) AF: 0.878 AC: 1855 AN: 2112

Alfa AF: 0.897 Hom.: 101279

Bravo AF: 0.873

Asia WGS AF: 0.826 AC: 2874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6721348; hg19: chr2-173118509;