5-180071634-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018434.6(RNF130):c.69G>C(p.Trp23Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000104 in 1,346,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018434.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF130 | NM_018434.6 | c.69G>C | p.Trp23Cys | missense_variant | 1/9 | ENST00000521389.6 | |
RNF130 | NM_001410829.1 | c.69G>C | p.Trp23Cys | missense_variant | 1/8 | ||
RNF130 | NM_001280801.2 | c.69G>C | p.Trp23Cys | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF130 | ENST00000521389.6 | c.69G>C | p.Trp23Cys | missense_variant | 1/9 | 1 | NM_018434.6 | P4 | |
RNF130 | ENST00000261947.4 | c.69G>C | p.Trp23Cys | missense_variant | 1/8 | 1 | A2 | ||
RNF130 | ENST00000520911.5 | c.69G>C | p.Trp23Cys | missense_variant, NMD_transcript_variant | 1/9 | 1 | |||
RNF130 | ENST00000522208.6 | c.69G>C | p.Trp23Cys | missense_variant | 1/8 | 5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000879 AC: 13AN: 147848Hom.: 0 AF XY: 0.0000471 AC XY: 4AN XY: 84866
GnomAD4 exome AF: 0.0000104 AC: 14AN: 1346062Hom.: 0 Cov.: 39 AF XY: 0.00000748 AC XY: 5AN XY: 668876
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.69G>C (p.W23C) alteration is located in exon 1 (coding exon 1) of the RNF130 gene. This alteration results from a G to C substitution at nucleotide position 69, causing the tryptophan (W) at amino acid position 23 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at