rs7723398

chr5-52933275-G-Achr5-52933275-G-C

Variant summary

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

The NM_181501.2(ITGA1):c.2862-619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,802 control chromosomes in the GnomAD database, including 6,156 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 0.27 (6156 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA1	NM_181501.2	c.2862-619G>A		intron_variant		ENST00000282588.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA1	ENST00000282588.7	c.2862-619G>A		intron_variant		1	NM_181501.2	P1
ITGA2-AS1	ENST00000662246.1	n.232-739C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40720 AN: 151684 Hom.: 6143 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.236

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.269 AC: 40762 AN: 151802 Hom.: 6156 Cov.: 32 AF XY: 0.263 AC XY: 19544 AN XY: 74178

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.238

Alfa AF: 0.245 Hom.: 2480

Bravo AF: 0.270

Asia WGS AF: 0.322 AC: 1117 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.047
Dann	Benign	0.36

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: rs7723398; hg19: chr5-52229105;