GeneBe

16-31356857-T-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000887.5(ITGAX):​c.247+129T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 667,536 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.000015 ( 0 hom. )

Consequence

ITGAX
NM_000887.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.565

Publications

31 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

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=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ITGAXNM_000887.5 linkc.247+129T>G intron_variant Intron 3 of 29 ENST00000268296.9 NP_000878.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ITGAXENST00000268296.9 linkc.247+129T>G intron_variant Intron 3 of 29 1 NM_000887.5 ENSP00000268296.5
ITGAXENST00000562522.2 linkc.247+129T>G intron_variant Intron 3 of 30 1 ENSP00000454623.1
ITGAXENST00000567409.1 linkn.314+129T>G intron_variant Intron 3 of 3 1
ITGAXENST00000562918.5 linkc.247+129T>G intron_variant Intron 3 of 4 2 ENSP00000483860.1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.0000150
AC:
10
AN:
667536
Hom.:
0
Cov.:
9
AF XY:
0.0000290
AC XY:
10
AN XY:
345304
show subpopulations
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:
0.000181
AC:
10
AN:
55278
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:
455106
Other (OTH)
AF:
0.00
AC:
0
AN:
33360
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.7
DANN
Benign
0.41
PhyloP100
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs7190997; hg19: chr16-31368178; API