rs150060415
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_000417.3(IL2RA):āc.691G>Cā(p.Glu231Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E231D) has been classified as Uncertain significance.
Frequency
Consequence
NM_000417.3 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 |
---|---|---|---|---|---|---|---|
IL2RA | NM_000417.3 | c.691G>C | p.Glu231Gln | missense_variant | 6/8 | ENST00000379959.8 | |
LOC124902368 | XR_007062042.1 | n.144-1872C>G | intron_variant, non_coding_transcript_variant | ||||
IL2RA | NM_001308242.2 | c.475G>C | p.Glu159Gln | missense_variant | 5/7 | ||
IL2RA | NM_001308243.2 | c.403G>C | p.Glu135Gln | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL2RA | ENST00000379959.8 | c.691G>C | p.Glu231Gln | missense_variant | 6/8 | 1 | NM_000417.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000558 AC: 85AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251492Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135920
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461420Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727078
GnomAD4 genome ? AF: 0.000558 AC: 85AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74482
ClinVar
Submissions by phenotype
Immunodeficiency due to CD25 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at