chr17-30971197-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032322.4(RNF135):c.124C>T(p.Arg42Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,524,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032322.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF135 | NM_032322.4 | c.124C>T | p.Arg42Cys | missense_variant | 1/5 | ENST00000328381.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF135 | ENST00000328381.10 | c.124C>T | p.Arg42Cys | missense_variant | 1/5 | 1 | NM_032322.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000305 AC: 36AN: 117888Hom.: 0 AF XY: 0.000307 AC XY: 20AN XY: 65152
GnomAD4 exome AF: 0.000161 AC: 221AN: 1372178Hom.: 0 Cov.: 31 AF XY: 0.000158 AC XY: 107AN XY: 676828
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.124C>T (p.R42C) alteration is located in exon 1 (coding exon 1) of the RNF135 gene. This alteration results from a C to T substitution at nucleotide position 124, causing the arginine (R) at amino acid position 42 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | RNF135: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at