rs1551943

chr5-52899203-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.1309+820G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,174 control chromosomes in the GnomAD database, including 2,543 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 0.17 (2543 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA1	NM_181501.2	c.1309+820G>A		intron_variant		ENST00000282588.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA1	ENST00000282588.7	c.1309+820G>A		intron_variant		1	NM_181501.2	P1
ITGA1	ENST00000650673.1	c.*471+820G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25333 AN: 152056 Hom.: 2545 Cov.: 32

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.167 AC: 25337 AN: 152174 Hom.: 2543 Cov.: 32 AF XY: 0.164 AC XY: 12235 AN XY: 74394

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.174

Alfa AF: 0.220 Hom.: 8307

Bravo AF: 0.158

Asia WGS AF: 0.205 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.3
Dann	Benign	0.80

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: rs1551943; hg19: chr5-52195033;