NM_181501.2:c.3078+979C>T

Variant names:

• chr5-52938493-C-T
• rs1871184
• NM_181501.2:c.3078+979C>T

Variant summary

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

The NM_181501.2(ITGA1):​c.3078+979C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,008 control chromosomes in the GnomAD database, including 1,514 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 0.14 (1514 hom., cov: 32)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 7 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]

ITGA2-AS1 (HGNC:40306): (ITGA2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA1	NM_181501.2	c.3078+979C>T		intron_variant	Intron 24 of 28	ENST00000282588.7	NP_852478.1
ITGA2-AS1	NR_186583.1	n.354-5957G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA1	ENST00000282588.7	c.3078+979C>T		intron_variant	Intron 24 of 28	1	NM_181501.2	ENSP00000282588.5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21403 AN: 151890 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.141 AC: 21412 AN: 152008 Hom.: 1514 Cov.: 32 AF XY: 0.141 AC XY: 10442 AN XY: 74308

African (AFR) AF: 0.134 AC: 5561 AN: 41442

American (AMR) AF: 0.150 AC: 2297 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3470

East Asian (EAS) AF: 0.157 AC: 813 AN: 5176

South Asian (SAS) AF: 0.159 AC: 765 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1664 AN: 10552

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9550 AN: 67962

Other (OTH) AF: 0.149 AC: 313 AN: 2104

Alfa AF: 0.139 Hom.: 753

Bravo AF: 0.142

Asia WGS AF: 0.152 AC: 526 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		0.36
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: rs1871184; hg19: chr5-52234323;