X-118758239-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001560.3(IL13RA1):c.673C>A(p.Arg225Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000761 in 998,145 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001560.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13RA1 | NM_001560.3 | c.673C>A | p.Arg225Ser | missense_variant | 5/11 | ENST00000371666.8 | |
IL13RA1 | XM_047442096.1 | c.673C>A | p.Arg225Ser | missense_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL13RA1 | ENST00000371666.8 | c.673C>A | p.Arg225Ser | missense_variant | 5/11 | 1 | NM_001560.3 | P1 | |
IL13RA1 | ENST00000371642.1 | c.673C>A | p.Arg225Ser | missense_variant | 5/6 | 1 | |||
IL13RA1 | ENST00000652600.1 | c.667C>A | p.Arg223Ser | missense_variant | 6/12 | ||||
IL13RA1 | ENST00000481868.1 | n.261C>A | non_coding_transcript_exon_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000403 AC: 45AN: 111583Hom.: 0 Cov.: 21 AF XY: 0.000384 AC XY: 13AN XY: 33815
GnomAD3 exomes AF: 0.000160 AC: 27AN: 168749Hom.: 0 AF XY: 0.000125 AC XY: 7AN XY: 56105
GnomAD4 exome AF: 0.0000350 AC: 31AN: 886562Hom.: 0 Cov.: 15 AF XY: 0.0000305 AC XY: 7AN XY: 229768
GnomAD4 genome ? AF: 0.000403 AC: 45AN: 111583Hom.: 0 Cov.: 21 AF XY: 0.000384 AC XY: 13AN XY: 33815
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.673C>A (p.R225S) alteration is located in exon 5 (coding exon 5) of the IL13RA1 gene. This alteration results from a C to A substitution at nucleotide position 673, causing the arginine (R) at amino acid position 225 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at