5-52810674-A-G

Variant names:

• chr5-52810674-A-G
• rs6881900
• NM_181501.2:c.61+22260A>G

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+22260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,144 control chromosomes in the GnomAD database, including 5,588 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 0.26 (5588 hom., cov: 33)
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA1	NM_181501.2	MANE Select	c.61+22260A>G		intron	N/A	NP_852478.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA1	ENST00000282588.7	TSL:1 MANE Select	c.61+22260A>G		intron	N/A	ENSP00000282588.5
	ITGA1	ENST00000504086.1	TSL:2	n.469-13639A>G		intron	N/A
	ITGA1	ENST00000650673.1		n.61+22260A>G		intron	N/A	ENSP00000498529.1

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40160 AN: 152026 Hom.: 5577 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.264 AC: 40198 AN: 152144 Hom.: 5588 Cov.: 33 AF XY: 0.261 AC XY: 19434 AN XY: 74374

African (AFR) AF: 0.217 AC: 9020 AN: 41496

American (AMR) AF: 0.215 AC: 3282 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1167 AN: 3472

East Asian (EAS) AF: 0.186 AC: 961 AN: 5164

South Asian (SAS) AF: 0.184 AC: 887 AN: 4824

European-Finnish (FIN) AF: 0.319 AC: 3373 AN: 10578

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

European-Non Finnish (NFE) AF: 0.304 AC: 20704 AN: 67998

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.269 Hom.: 2904

Bravo AF: 0.258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.64
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: rs6881900; hg19: chr5-52106508;