rs4053043
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000391491.2(RPL15P3):n.199C>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0000186 in 1,613,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
RPL15P3
ENST00000391491.2 non_coding_transcript_exon
ENST00000391491.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.89
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL15P3 | ENST00000391491.2 | n.199C>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152180Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461104Hom.: 0 Cov.: 34 AF XY: 0.00000688 AC XY: 5AN XY: 726864
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152298Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74480
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at