X-115013854-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000640.3(IL13RA2):c.436G>A(p.Val146Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,004,779 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 39 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000640.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL13RA2 | ENST00000243213.2 | c.436G>A | p.Val146Ile | missense_variant | Exon 5 of 10 | 1 | NM_000640.3 | ENSP00000243213.1 | ||
IL13RA2 | ENST00000371936.5 | c.436G>A | p.Val146Ile | missense_variant | Exon 6 of 11 | 5 | ENSP00000361004.1 |
Frequencies
GnomAD3 genomes AF: 0.0000536 AC: 6AN: 111859Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 34041
GnomAD3 exomes AF: 0.0000564 AC: 10AN: 177288Hom.: 0 AF XY: 0.0000965 AC XY: 6AN XY: 62204
GnomAD4 exome AF: 0.000118 AC: 105AN: 892920Hom.: 0 Cov.: 17 AF XY: 0.000137 AC XY: 35AN XY: 254600
GnomAD4 genome AF: 0.0000536 AC: 6AN: 111859Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 34041
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at