chr10-5966186-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002189.4(IL15RA):c.242C>T(p.Thr81Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,002 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002189.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL15RA | NM_002189.4 | c.242C>T | p.Thr81Met | missense_variant | 2/7 | ENST00000379977.8 | |
LOC107984200 | XR_001747348.2 | n.1458+1865G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL15RA | ENST00000379977.8 | c.242C>T | p.Thr81Met | missense_variant | 2/7 | 1 | NM_002189.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251286Hom.: 1 AF XY: 0.0000442 AC XY: 6AN XY: 135808
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1460738Hom.: 1 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 726388
GnomAD4 genome AF: 0.000131 AC: 20AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.242C>T (p.T81M) alteration is located in exon 2 (coding exon 2) of the IL15RA gene. This alteration results from a C to T substitution at nucleotide position 242, causing the threonine (T) at amino acid position 81 to be replaced by a methionine (M). 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