chr17-30971417-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032322.4(RNF135):c.344G>A(p.Arg115Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0192 in 1,516,774 control chromosomes in the GnomAD database, including 351 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_032322.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF135 | NM_032322.4 | c.344G>A | p.Arg115Lys | missense_variant | 1/5 | ENST00000328381.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF135 | ENST00000328381.10 | c.344G>A | p.Arg115Lys | missense_variant | 1/5 | 1 | NM_032322.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0143 AC: 2182AN: 152200Hom.: 18 Cov.: 33
GnomAD3 exomes AF: 0.0124 AC: 1373AN: 110488Hom.: 20 AF XY: 0.0119 AC XY: 735AN XY: 61648
GnomAD4 exome AF: 0.0197 AC: 26909AN: 1364464Hom.: 333 Cov.: 31 AF XY: 0.0192 AC XY: 12944AN XY: 673386
GnomAD4 genome ? AF: 0.0143 AC: 2182AN: 152310Hom.: 18 Cov.: 33 AF XY: 0.0141 AC XY: 1048AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 28, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 23, 2017 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 06, 2020 | This variant is associated with the following publications: (PMID: 26368817) - |
RNF135-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 13, 2019 | This variant is classified as 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