rs4972741

Variant names:

• chr2-172250932-G-A
• rs4972741
• ENST00000715295.1:c.-536+16675G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-172250932-G-A
• chr2-172250932-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+16675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,088 control chromosomes in the GnomAD database, including 58,963 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 (58963 hom., cov: 30)
• Consequence: ITGA6 ENST00000715295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 5 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]

LOC107985960 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715295.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA6	ENST00000715295.1		c.-536+16675G>A		intron	N/A	ENSP00000520448.1
	DLX2-DT	ENST00000662340.1		n.213-47265G>A		intron	N/A
	DLX2-DT	ENST00000667725.1		n.242-47265G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133622 AN: 151970 Hom.: 58939 Cov.: 30

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.879 AC: 133693 AN: 152088 Hom.: 58963 Cov.: 30 AF XY: 0.882 AC XY: 65547 AN XY: 74338

African (AFR) AF: 0.806 AC: 33416 AN: 41440

American (AMR) AF: 0.902 AC: 13785 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3178 AN: 3472

East Asian (EAS) AF: 0.882 AC: 4556 AN: 5168

South Asian (SAS) AF: 0.846 AC: 4072 AN: 4812

European-Finnish (FIN) AF: 0.924 AC: 9771 AN: 10574

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61937 AN: 68024

Other (OTH) AF: 0.882 AC: 1862 AN: 2112

Alfa AF: 0.895 Hom.: 10626

Bravo AF: 0.876

Asia WGS AF: 0.826 AC: 2875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4972741; hg19: chr2-173115660;