16-18789006-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001019.5(RPS15A):āc.108G>Cā(p.Arg36=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,613,416 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. R36R) has been classified as Likely benign.
Frequency
Consequence
NM_001019.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS15A | NM_001019.5 | c.108G>C | p.Arg36= | synonymous_variant | 2/5 | ENST00000322989.8 | |
RPS15A | NM_001030009.2 | c.108G>C | p.Arg36= | synonymous_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS15A | ENST00000322989.8 | c.108G>C | p.Arg36= | synonymous_variant | 2/5 | 1 | NM_001019.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000136 AC: 34AN: 250662Hom.: 1 AF XY: 0.000177 AC XY: 24AN XY: 135474
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461230Hom.: 3 Cov.: 31 AF XY: 0.000109 AC XY: 79AN XY: 726918
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74348
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 18, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | RPS15A: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at