chr5-52831919-G-C

Variant names:

• chr5-52831919-G-C
• rs17211331
• NM_181501.2:c.62-17446G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181501.2(ITGA1):​c.62-17446G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,982 control chromosomes in the GnomAD database, including 1,126 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 0.12 (1126 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 0 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA1	NM_181501.2	c.62-17446G>C		intron_variant	Intron 1 of 28	ENST00000282588.7	NP_852478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA1	ENST00000282588.7	c.62-17446G>C		intron_variant	Intron 1 of 28	1	NM_181501.2	ENSP00000282588.5
ITGA1	ENST00000650673.1	n.62-17446G>C		intron_variant	Intron 1 of 28			ENSP00000498529.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18145 AN: 151864 Hom.: 1125 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.119 AC: 18148 AN: 151982 Hom.: 1126 Cov.: 32 AF XY: 0.120 AC XY: 8904 AN XY: 74290

African (AFR) AF: 0.115 AC: 4759 AN: 41450

American (AMR) AF: 0.173 AC: 2641 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3470

East Asian (EAS) AF: 0.0869 AC: 448 AN: 5158

South Asian (SAS) AF: 0.141 AC: 679 AN: 4814

European-Finnish (FIN) AF: 0.0888 AC: 938 AN: 10564

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8020 AN: 67962

Other (OTH) AF: 0.120 AC: 254 AN: 2112

Alfa AF: 0.117 Hom.: 123

Bravo AF: 0.123

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.47
PhyloP100		0.33
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: rs17211331; hg19: chr5-52127753;