chr5-52899203-G-A

Variant names:

• chr5-52899203-G-A
• rs1551943
• NM_181501.2:c.1309+820G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ITGA1	NM_181501.2	c.1309+820G>A		intron_variant	Intron 11 of 28	ENST00000282588.7	NP_852478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA1	ENST00000282588.7	c.1309+820G>A		intron_variant	Intron 11 of 28	1	NM_181501.2	ENSP00000282588.5
ITGA1	ENST00000650673.1	n.*471+820G>A		intron_variant	Intron 11 of 28			ENSP00000498529.1

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

African (AFR) AF: 0.0625 AC: 2597 AN: 41542

American (AMR) AF: 0.137 AC: 2096 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3468

East Asian (EAS) AF: 0.168 AC: 870 AN: 5180

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1686 AN: 10592

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15163 AN: 67972

Other (OTH) AF: 0.174 AC: 366 AN: 2108

Alfa AF: 0.209 Hom.: 11848

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
PhyloP100		0.0070
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1551943; hg19: chr5-52195033;