rs7723398

Variant names:

• chr5-52933275-G-A
• rs7723398
• NM_181501.2:c.2862-619G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-52933275-G-A
• chr5-52933275-G-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.2862-619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,802 control chromosomes in the GnomAD database, including 6,156 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 (6156 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ITGA1 NM_181501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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.2862-619G>A		intron	N/A	NP_852478.1
	ITGA2-AS1	NR_186583.1		n.354-739C>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.2862-619G>A		intron	N/A	ENSP00000282588.5
	ITGA1	ENST00000506275.1	TSL:1	n.2124G>A		non_coding_transcript_exon	Exon 1 of 7
	ITGA1	ENST00000504669.5	TSL:1	n.5537-619G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40720 AN: 151684 Hom.: 6143 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.236

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.269 AC: 40762 AN: 151802 Hom.: 6156 Cov.: 32 AF XY: 0.263 AC XY: 19544 AN XY: 74178

African (AFR) AF: 0.396 AC: 16403 AN: 41390

American (AMR) AF: 0.163 AC: 2491 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 685 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1155 AN: 5160

South Asian (SAS) AF: 0.372 AC: 1791 AN: 4810

European-Finnish (FIN) AF: 0.151 AC: 1595 AN: 10552

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15812 AN: 67866

Other (OTH) AF: 0.238 AC: 502 AN: 2110

Alfa AF: 0.244 Hom.: 2700

Bravo AF: 0.270

Asia WGS AF: 0.322 AC: 1117 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.047
DANN	Benign	0.36
PhyloP100		-1.3
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: rs7723398; hg19: chr5-52229105;