5-180071678-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018434.6(RNF130):c.25C>T(p.Pro9Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000924 in 1,407,268 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_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.25C>T | p.Pro9Ser | missense_variant | 1/9 | ENST00000521389.6 | |
RNF130 | NM_001410829.1 | c.25C>T | p.Pro9Ser | missense_variant | 1/8 | ||
RNF130 | NM_001280801.2 | c.25C>T | p.Pro9Ser | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF130 | ENST00000521389.6 | c.25C>T | p.Pro9Ser | missense_variant | 1/9 | 1 | NM_018434.6 | P4 | |
RNF130 | ENST00000261947.4 | c.25C>T | p.Pro9Ser | missense_variant | 1/8 | 1 | A2 | ||
RNF130 | ENST00000520911.5 | c.25C>T | p.Pro9Ser | missense_variant, NMD_transcript_variant | 1/9 | 1 | |||
RNF130 | ENST00000522208.6 | c.25C>T | p.Pro9Ser | missense_variant | 1/8 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150490Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000955 AC: 12AN: 1256778Hom.: 0 Cov.: 33 AF XY: 0.00000807 AC XY: 5AN XY: 619746
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150490Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.25C>T (p.P9S) alteration is located in exon 1 (coding exon 1) of the RNF130 gene. This alteration results from a C to T substitution at nucleotide position 25, causing the proline (P) at amino acid position 9 to be replaced by a serine (S). 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