chr5-52897294-A-G

Position:

• chr5-52897294-A-G

Variant summary

Our verdict is Benign. Variant got -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

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA1	NM_181501.2	c.1091-161A>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.1091-161A>G		intron_variant		1	NM_181501.2	ENSP00000282588	P1
ITGA1	ENST00000650673.1	c.*253-161A>G		intron_variant, NMD_transcript_variant				ENSP00000498529

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

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.0665

Gnomad4 SAS AF: 0.0602

Gnomad4 FIN AF: 0.0666

Gnomad4 NFE AF: 0.0857

Gnomad4 OTH AF: 0.0876

Alfa AF: 0.0847 Hom.: 1086

Bravo AF: 0.0657

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs4074793; hg19: chr5-52193125;