rs5956080
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001560.3(IL13RA1):c.89-3517T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0984 in 110,846 control chromosomes in the GnomAD database, including 1,396 homozygotes. There are 2,736 hemizygotes in GnomAD. 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
Consequence
NM_001560.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13RA1 | NM_001560.3 | c.89-3517T>G | intron_variant | ENST00000371666.8 | |||
IL13RA1 | XM_047442096.1 | c.89-3517T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL13RA1 | ENST00000371666.8 | c.89-3517T>G | intron_variant | 1 | NM_001560.3 | P1 | |||
IL13RA1 | ENST00000371642.1 | c.89-3517T>G | intron_variant | 1 | |||||
IL13RA1 | ENST00000652600.1 | c.1-2653T>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0984 AC: 10899AN: 110794Hom.: 1393 Cov.: 23 AF XY: 0.0825 AC XY: 2730AN XY: 33086
GnomAD4 genome ? AF: 0.0984 AC: 10911AN: 110846Hom.: 1396 Cov.: 23 AF XY: 0.0825 AC XY: 2736AN XY: 33148
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at