rs2929

Variant names:

• chr16-31381987-G-A
• rs2929
• NM_000887.5:c.*80G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-31381987-G-A
• chr16-31381987-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000887.5(ITGAX):​c.*80G>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 0.226 in 1,474,592 control chromosomes in the GnomAD database, including 39,157 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 (5703 hom., cov: 26)
  • Exomes 𝑓: 0.22 (33454 hom.)
• Consequence: ITGAX NM_000887.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 18 publications found

Genes affected

ITGAX (HGNC:6152): (integrin subunit alpha X) This gene encodes the integrin alpha X chain protein. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein combines with the beta 2 chain (ITGB2) to form a leukocyte-specific integrin referred to as inactivated-C3b (iC3b) receptor 4 (CR4). The alpha X beta 2 complex seems to overlap the properties of the alpha M beta 2 integrin in the adherence of neutrophils and monocytes to stimulated endothelium cells, and in the phagocytosis of complement coated particles. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000887.5. 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
	ITGAX	NM_000887.5	MANE Select	c.*80G>A		3_prime_UTR	Exon 30 of 30	NP_000878.2
	ITGAX	NM_001286375.2		c.3481+91G>A		intron	N/A	NP_001273304.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGAX	ENST00000268296.9	TSL:1 MANE Select	c.*80G>A		3_prime_UTR	Exon 30 of 30	ENSP00000268296.5
	ITGAX	ENST00000562522.2	TSL:1	c.3481+91G>A		intron	N/A	ENSP00000454623.1
	ITGAX	ENST00000571644.1	TSL:2	n.3437G>A		non_coding_transcript_exon	Exon 22 of 22

Frequencies

GnomAD3 genomes AF: 0.275 AC: 38891 AN: 141454 Hom.: 5699 Cov.: 26

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.238

GnomAD4 exome AF: 0.221 AC: 294736 AN: 1333020 Hom.: 33454 Cov.: 21 AF XY: 0.220 AC XY: 144527 AN XY: 658026

African (AFR) AF: 0.425 AC: 12925 AN: 30420

American (AMR) AF: 0.139 AC: 4657 AN: 33468

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 3809 AN: 21866

East Asian (EAS) AF: 0.265 AC: 9573 AN: 36106

South Asian (SAS) AF: 0.164 AC: 11856 AN: 72302

European-Finnish (FIN) AF: 0.237 AC: 11273 AN: 47622

Middle Eastern (MID) AF: 0.163 AC: 636 AN: 3910

European-Non Finnish (NFE) AF: 0.221 AC: 227812 AN: 1032212

Other (OTH) AF: 0.221 AC: 12195 AN: 55114

GnomAD4 genome AF: 0.275 AC: 38919 AN: 141572 Hom.: 5703 Cov.: 26 AF XY: 0.270 AC XY: 18584 AN XY: 68886

African (AFR) AF: 0.429 AC: 16631 AN: 38728

American (AMR) AF: 0.173 AC: 2409 AN: 13962

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 567 AN: 3170

East Asian (EAS) AF: 0.204 AC: 938 AN: 4590

South Asian (SAS) AF: 0.172 AC: 738 AN: 4282

European-Finnish (FIN) AF: 0.255 AC: 2526 AN: 9900

Middle Eastern (MID) AF: 0.191 AC: 53 AN: 278

European-Non Finnish (NFE) AF: 0.224 AC: 14276 AN: 63858

Other (OTH) AF: 0.238 AC: 459 AN: 1932

Alfa AF: 0.223 Hom.: 18346

Bravo AF: 0.262

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		0.14
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: rs2929; hg19: chr16-31393308; COSMIC: COSV107270975;