rs796051887
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_000417.3(IL2RA):c.497G>A(p.Ser166Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. S166S) has been classified as Likely benign.
Frequency
Consequence
NM_000417.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL2RA | NM_000417.3 | c.497G>A | p.Ser166Asn | missense_variant | 4/8 | ENST00000379959.8 | |
IL2RA | NM_001308242.2 | c.368-1623G>A | intron_variant | ||||
IL2RA | NM_001308243.2 | c.368-2065G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL2RA | ENST00000379959.8 | c.497G>A | p.Ser166Asn | missense_variant | 4/8 | 1 | NM_000417.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461890Hom.: 0 Cov.: 35 AF XY: 0.00000550 AC XY: 4AN XY: 727244
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Immunodeficiency due to CD25 deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at