rs1871184

chr5-52938493-C-T

Variant summary

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

The NM_181501.2(ITGA1):c.3078+979C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,008 control chromosomes in the GnomAD database, including 1,514 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 0.14 (1514 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

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]

ITGA2-AS1 (HGNC:40306): (ITGA2 antisense RNA 1)

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 (SAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA1	NM_181501.2	c.3078+979C>T		intron_variant		ENST00000282588.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA1	ENST00000282588.7	c.3078+979C>T		intron_variant		1	NM_181501.2	P1
ITGA2-AS1	ENST00000662246.1	n.232-5957G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21403 AN: 151890 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.141 AC: 21412 AN: 152008 Hom.: 1514 Cov.: 32 AF XY: 0.141 AC XY: 10442 AN XY: 74308

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.149

Alfa AF: 0.140 Hom.: 678

Bravo AF: 0.142

Asia WGS AF: 0.152 AC: 526 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.8
Dann	Benign	0.57

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: rs1871184; hg19: chr5-52234323;