rs889295

Variant names:

• chr5-52814876-A-G
• rs889295
• NM_181501.2:c.61+26462A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181501.2. 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
	ITGA1	NM_181501.2	MANE Select	c.61+26462A>G		intron	N/A	NP_852478.1	P56199

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA1	ENST00000282588.7	TSL:1 MANE Select	c.61+26462A>G		intron	N/A	ENSP00000282588.5	P56199
	ITGA1	ENST00000504086.1	TSL:2	n.469-9437A>G		intron	N/A
	ITGA1	ENST00000650673.1		n.61+26462A>G		intron	N/A	ENSP00000498529.1	A0A494C0F7

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

African (AFR) AF: 0.658 AC: 27267 AN: 41436

American (AMR) AF: 0.499 AC: 7617 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1892 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1815 AN: 5162

South Asian (SAS) AF: 0.477 AC: 2301 AN: 4820

European-Finnish (FIN) AF: 0.589 AC: 6220 AN: 10562

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37842 AN: 67942

Other (OTH) AF: 0.546 AC: 1153 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.0
DANN	Benign	0.64
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs889295; hg19: chr5-52110710;