18-32037158-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_017831.4(RNF125):c.207G>A(p.Lys69=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,454,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017831.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF125 | NM_017831.4 | c.207G>A | p.Lys69= | synonymous_variant | 2/6 | ENST00000217740.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF125 | ENST00000217740.4 | c.207G>A | p.Lys69= | synonymous_variant | 2/6 | 1 | NM_017831.4 | P1 | |
RNF125 | ENST00000580209.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1454966Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 723740
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
RNF125-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 01, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.