NM_181501.2:c.62-13884T>C

Variant names:

• chr5-52835481-T-C
• rs2432143
• NM_181501.2:c.62-13884T>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.62-13884T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,168 control chromosomes in the GnomAD database, including 948 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 0.11 (948 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181501.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA1	NM_181501.2	MANE Select	c.62-13884T>C		intron	N/A	NP_852478.1	P56199

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA1	ENST00000282588.7	TSL:1 MANE Select	c.62-13884T>C		intron	N/A	ENSP00000282588.5	P56199
	ITGA1	ENST00000650673.1		n.62-13884T>C		intron	N/A	ENSP00000498529.1	A0A494C0F7

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16455 AN: 152050 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.108 AC: 16479 AN: 152168 Hom.: 948 Cov.: 32 AF XY: 0.107 AC XY: 7991 AN XY: 74398

African (AFR) AF: 0.119 AC: 4948 AN: 41508

American (AMR) AF: 0.101 AC: 1550 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3470

East Asian (EAS) AF: 0.178 AC: 920 AN: 5156

South Asian (SAS) AF: 0.113 AC: 545 AN: 4830

European-Finnish (FIN) AF: 0.0726 AC: 770 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7054 AN: 67996

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.106 Hom.: 1953

Bravo AF: 0.111

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.29
PhyloP100		-0.034
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: rs2432143; hg19: chr5-52131315;