rs3762619

Positions:

• chr2-172441157-G-A
• chr2-172441157-G-C

Variant summary

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

The NM_001394928.1(ITGA6):​c.182+13187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 152,122 control chromosomes in the GnomAD database, including 1,359 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 0.082 (1359 hom., cov: 32)
• Consequence: ITGA6 NM_001394928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA6	NM_000210.4	c.182+13187G>A		intron_variant		ENST00000684293.1
ITGA6	NM_001394928.1	c.182+13187G>A		intron_variant		ENST00000442250.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA6	ENST00000442250.6	c.182+13187G>A		intron_variant		5	NM_001394928.1
ITGA6	ENST00000684293.1	c.182+13187G>A		intron_variant			NM_000210.4	P3

Frequencies

GnomAD3 genomes AF: 0.0824 AC: 12522 AN: 152004 Hom.: 1362 Cov.: 32

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0823 AC: 12523 AN: 152122 Hom.: 1359 Cov.: 32 AF XY: 0.0945 AC XY: 7025 AN XY: 74356

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0328 Hom.: 34

Bravo AF: 0.0783

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762619; hg19: chr2-173305885;