NM_181501.2:c.61+20515C>T

Variant names:

• chr5-52808929-C-T
• rs10512997
• NM_181501.2:c.61+20515C>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.61+20515C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,358 control chromosomes in the GnomAD database, including 5,578 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 0.27 (5578 hom., cov: 30)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• 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]

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 (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA1	NM_181501.2	c.61+20515C>T		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.61+20515C>T		intron_variant	Intron 1 of 28	1	NM_181501.2	ENSP00000282588.5
ITGA1	ENST00000504086.1	n.469-15384C>T		intron_variant	Intron 1 of 1	2
ITGA1	ENST00000650673.1	n.61+20515C>T		intron_variant	Intron 1 of 28			ENSP00000498529.1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40077 AN: 151240 Hom.: 5567 Cov.: 30

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.265 AC: 40116 AN: 151358 Hom.: 5578 Cov.: 30 AF XY: 0.262 AC XY: 19385 AN XY: 73968

African (AFR) AF: 0.220 AC: 8994 AN: 40920

American (AMR) AF: 0.215 AC: 3279 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3466

East Asian (EAS) AF: 0.185 AC: 957 AN: 5160

South Asian (SAS) AF: 0.185 AC: 892 AN: 4826

European-Finnish (FIN) AF: 0.319 AC: 3343 AN: 10488

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20686 AN: 67918

Other (OTH) AF: 0.266 AC: 562 AN: 2110

Alfa AF: 0.290 Hom.: 3331

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		0.080
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: rs10512997; hg19: chr5-52104763;