rs2432143

Positions:

• chr5-52835481-T-C

Variant summary

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

The NM_181501.2(ITGA1):​c.62-13884T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,168 control chromosomes in the GnomAD database, including 948 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 0.11 (948 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA1	NM_181501.2	c.62-13884T>C		intron_variant		ENST00000282588.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA1	ENST00000282588.7	c.62-13884T>C		intron_variant		1	NM_181501.2	P1
ITGA1	ENST00000650673.1	c.62-13884T>C		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16455 AN: 152050 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.108 AC: 16479 AN: 152168 Hom.: 948 Cov.: 32 AF XY: 0.107 AC XY: 7991 AN XY: 74398

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0726

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.112

Alfa AF: 0.104 Hom.: 1313

Bravo AF: 0.111

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.29

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: rs2432143; hg19: chr5-52131315;