chr10-5953184-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002189.4(IL15RA):c.715G>A(p.Val239Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000795 in 1,614,152 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002189.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL15RA | NM_002189.4 | c.715G>A | p.Val239Ile | missense_variant | 7/7 | ENST00000379977.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL15RA | ENST00000379977.8 | c.715G>A | p.Val239Ile | missense_variant | 7/7 | 1 | NM_002189.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00359 AC: 547AN: 152222Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00122 AC: 304AN: 249130Hom.: 2 AF XY: 0.000845 AC XY: 114AN XY: 134888
GnomAD4 exome AF: 0.000504 AC: 737AN: 1461812Hom.: 3 Cov.: 31 AF XY: 0.000421 AC XY: 306AN XY: 727216
GnomAD4 genome AF: 0.00359 AC: 547AN: 152340Hom.: 5 Cov.: 33 AF XY: 0.00327 AC XY: 244AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 04, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at