rs7190997

Variant names:

• chr16-31356857-T-A
• rs7190997
• NM_000887.5:c.247+129T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-31356857-T-A
• chr16-31356857-T-C
• chr16-31356857-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000887.5(ITGAX):​c.247+129T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITGAX NM_000887.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 31 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGAX	NM_000887.5	c.247+129T>A		intron_variant	Intron 3 of 29	ENST00000268296.9	NP_000878.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGAX	ENST00000268296.9	c.247+129T>A		intron_variant	Intron 3 of 29	1	NM_000887.5	ENSP00000268296.5
ITGAX	ENST00000562522.2	c.247+129T>A		intron_variant	Intron 3 of 30	1		ENSP00000454623.1
ITGAX	ENST00000567409.1	n.314+129T>A		intron_variant	Intron 3 of 3	1
ITGAX	ENST00000562918.5	c.247+129T>A		intron_variant	Intron 3 of 4	2		ENSP00000483860.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 667536 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 345304

African (AFR) AF: 0.00 AC: 0 AN: 16618

American (AMR) AF: 0.00 AC: 0 AN: 22154

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16044

East Asian (EAS) AF: 0.00 AC: 0 AN: 32316

South Asian (SAS) AF: 0.00 AC: 0 AN: 55280

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34162

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2498

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 455104

Other (OTH) AF: 0.00 AC: 0 AN: 33360

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.60
PhyloP100		0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs7190997; hg19: chr16-31368178;