5-52897294-A-G

Variant names:

• chr5-52897294-A-G
• rs4074793
• NM_181501.2:c.1091-161A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_181501.2(ITGA1):​c.1091-161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0669 in 152,250 control chromosomes in the GnomAD database, including 422 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 0.067 (422 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.826
• Publications: 26 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0982 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.1091-161A>G		intron	N/A	NP_852478.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA1	ENST00000282588.7	TSL:1 MANE Select	c.1091-161A>G		intron	N/A	ENSP00000282588.5
	ITGA1	ENST00000650673.1		n.*253-161A>G		intron	N/A	ENSP00000498529.1

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10191 AN: 152132 Hom.: 421 Cov.: 32

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0856

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0669 AC: 10189 AN: 152250 Hom.: 422 Cov.: 32 AF XY: 0.0677 AC XY: 5044 AN XY: 74462

African (AFR) AF: 0.0191 AC: 793 AN: 41538

American (AMR) AF: 0.102 AC: 1566 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3470

East Asian (EAS) AF: 0.0665 AC: 345 AN: 5186

South Asian (SAS) AF: 0.0602 AC: 291 AN: 4830

European-Finnish (FIN) AF: 0.0666 AC: 707 AN: 10612

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0857 AC: 5825 AN: 68000

Other (OTH) AF: 0.0876 AC: 185 AN: 2112

Alfa AF: 0.0798 Hom.: 1674

Bravo AF: 0.0657

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.78
PhyloP100		0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.27		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.27		Position offset: -8

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

Other links and lift over

dbSNP: rs4074793; hg19: chr5-52193125;