chr1-218307594-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016052.4(RRP15):c.667G>A(p.Glu223Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,461,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016052.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RRP15 | NM_016052.4 | c.667G>A | p.Glu223Lys | missense_variant | 4/5 | ENST00000366932.4 | |
RRP15 | XM_047421797.1 | c.676G>A | p.Glu226Lys | missense_variant | 4/5 | ||
RRP15 | XM_011509597.4 | c.667G>A | p.Glu223Lys | missense_variant | 4/5 | ||
RRP15 | XM_047421798.1 | c.676G>A | p.Glu226Lys | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RRP15 | ENST00000366932.4 | c.667G>A | p.Glu223Lys | missense_variant | 4/5 | 1 | NM_016052.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251078Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135710
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461656Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727124
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at