rs1833556

Variant names:

• chr5-52955424-C-A
• rs1833556
• NM_181501.2:c.*2973C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-52955424-C-A
• chr5-52955424-C-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.*2973C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 151,998 control chromosomes in the GnomAD database, including 893 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 0.083 (893 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITGA1 NM_181501.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 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.*2973C>A		3_prime_UTR	Exon 29 of 29	NP_852478.1	P56199
	ITGA2-AS1	NR_186583.1		n.271-6517G>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.*2973C>A		3_prime_UTR	Exon 29 of 29	ENSP00000282588.5	P56199
	ITGA1	ENST00000506275.1	TSL:1	n.6394C>A		non_coding_transcript_exon	Exon 7 of 7
	ITGA1	ENST00000650673.1		n.*5675C>A		non_coding_transcript_exon	Exon 29 of 29	ENSP00000498529.1	A0A494C0F7

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12546 AN: 151880 Hom.: 893 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0230

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0709

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 62 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 38

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) AF: 0.00 AC: 0 AN: 60

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0826 AC: 12555 AN: 151998 Hom.: 893 Cov.: 32 AF XY: 0.0807 AC XY: 5998 AN XY: 74280

African (AFR) AF: 0.184 AC: 7609 AN: 41408

American (AMR) AF: 0.0665 AC: 1016 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0230 AC: 80 AN: 3472

East Asian (EAS) AF: 0.146 AC: 755 AN: 5160

South Asian (SAS) AF: 0.0453 AC: 218 AN: 4816

European-Finnish (FIN) AF: 0.0414 AC: 437 AN: 10568

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0334 AC: 2273 AN: 67986

Other (OTH) AF: 0.0706 AC: 149 AN: 2110

Alfa AF: 0.0409 Hom.: 98

Bravo AF: 0.0911

Asia WGS AF: 0.0970 AC: 338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.88
DANN	Benign	0.31
PhyloP100		-0.061
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: rs1833556; hg19: chr5-52251254;