chr5-52944142-G-A

Variant names:

• chr5-52944142-G-A
• rs13179969
• NM_181501.2:c.3286-801G>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.3286-801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,100 control chromosomes in the GnomAD database, including 2,646 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 0.18 (2646 hom., cov: 31)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 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.3286-801G>A		intron	N/A	NP_852478.1	P56199
	ITGA2-AS1	NR_186583.1		n.353+4683C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA1	ENST00000282588.7	TSL:1 MANE Select	c.3286-801G>A		intron	N/A	ENSP00000282588.5	P56199
	ITGA1	ENST00000504669.5	TSL:1	n.5961-801G>A		intron	N/A
	ITGA1	ENST00000506275.1	TSL:1	n.3167-801G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26755 AN: 151982 Hom.: 2643 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.176 AC: 26755 AN: 152100 Hom.: 2646 Cov.: 31 AF XY: 0.175 AC XY: 13029 AN XY: 74352

African (AFR) AF: 0.108 AC: 4473 AN: 41502

American (AMR) AF: 0.166 AC: 2541 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3470

East Asian (EAS) AF: 0.0897 AC: 462 AN: 5150

South Asian (SAS) AF: 0.102 AC: 492 AN: 4814

European-Finnish (FIN) AF: 0.232 AC: 2453 AN: 10584

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14503 AN: 67982

Other (OTH) AF: 0.198 AC: 418 AN: 2108

Alfa AF: 0.190 Hom.: 349

Bravo AF: 0.171

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.40
PhyloP100		-0.52
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: rs13179969; hg19: chr5-52239972;