rs13179969

chr5-52944142-G-A

Variant summary

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

The NM_181501.2(ITGA1):c.3286-801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,100 control chromosomes in the GnomAD database, including 2,646 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 0.18 (2646 hom., cov: 31)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA1	NM_181501.2	c.3286-801G>A		intron_variant		ENST00000282588.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA1	ENST00000282588.7	c.3286-801G>A		intron_variant		1	NM_181501.2	P1
ITGA2-AS1	ENST00000662246.1	n.231+4683C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26755 AN: 151982 Hom.: 2643 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.176 AC: 26755 AN: 152100 Hom.: 2646 Cov.: 31 AF XY: 0.175 AC XY: 13029 AN XY: 74352

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0897

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.198

Alfa AF: 0.190 Hom.: 349

Bravo AF: 0.171

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.87
Dann	Benign	0.40

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: rs13179969; hg19: chr5-52239972;