rs889295

Positions:

• chr5-52814876-A-G

Variant summary

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

The NM_181501.2(ITGA1):​c.61+26462A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,986 control chromosomes in the GnomAD database, including 25,171 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 0.57 (25171 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

Genes affected

ITGA1 (HGNC:6134): (integrin subunit alpha 1) This gene encodes the alpha 1 subunit of integrin receptors. This protein heterodimerizes with the beta 1 subunit to form a cell-surface receptor for collagen and laminin. The heterodimeric receptor is involved in cell-cell adhesion and may play a role in inflammation and fibrosis. The alpha 1 subunit contains an inserted (I) von Willebrand factor type I domain which is thought to be involved in collagen binding. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA1	NM_181501.2	c.61+26462A>G		intron_variant		ENST00000282588.7	NP_852478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA1	ENST00000282588.7	c.61+26462A>G		intron_variant		1	NM_181501.2	ENSP00000282588	P1
ITGA1	ENST00000650673.1	c.61+26462A>G		intron_variant, NMD_transcript_variant				ENSP00000498529
ITGA1	ENST00000504086.1	n.469-9437A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86508 AN: 151868 Hom.: 25143 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.570 AC: 86578 AN: 151986 Hom.: 25171 Cov.: 32 AF XY: 0.565 AC XY: 41989 AN XY: 74328

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.546

Alfa AF: 0.568 Hom.: 6572

Bravo AF: 0.568

Asia WGS AF: 0.444 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.0
DANN	Benign	0.64

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: rs889295; hg19: chr5-52110710;