chr10-5960507-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.443C>T(p.Pro148Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000284 in 1,614,156 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.443C>T | p.Pro148Leu | missense_variant | 4/7 | ENST00000379977.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL15RA | ENST00000379977.8 | c.443C>T | p.Pro148Leu | missense_variant | 4/7 | 1 | NM_002189.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000282 AC: 71AN: 251464Hom.: 0 AF XY: 0.000331 AC XY: 45AN XY: 135908
GnomAD4 exome AF: 0.000286 AC: 418AN: 1461862Hom.: 1 Cov.: 34 AF XY: 0.000304 AC XY: 221AN XY: 727234
GnomAD4 genome AF: 0.000263 AC: 40AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2023 | The c.443C>T (p.P148L) alteration is located in exon 4 (coding exon 4) of the IL15RA gene. This alteration results from a C to T substitution at nucleotide position 443, causing the proline (P) at amino acid position 148 to be replaced by a leucine (L). 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