5-179966896-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018434.6(RNF130):c.1060C>G(p.Leu354Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000218 in 1,614,118 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 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.1060C>G | p.Leu354Val | missense_variant | 7/9 | ENST00000521389.6 | |
RNF130 | NM_001410829.1 | c.1060C>G | p.Leu354Val | missense_variant | 7/8 | ||
RNF130 | NM_001280801.2 | c.1060C>G | p.Leu354Val | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF130 | ENST00000521389.6 | c.1060C>G | p.Leu354Val | missense_variant | 7/9 | 1 | NM_018434.6 | P4 | |
RNF130 | ENST00000261947.4 | c.1060C>G | p.Leu354Val | missense_variant | 7/8 | 1 | A2 | ||
RNF130 | ENST00000520911.5 | c.*579C>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 1 | ||||
RNF130 | ENST00000522208.6 | c.1060C>G | p.Leu354Val | missense_variant | 7/8 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251484Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135918
GnomAD4 exome AF: 0.000233 AC: 341AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.000216 AC XY: 157AN XY: 727248
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2022 | The c.1060C>G (p.L354V) alteration is located in exon 7 (coding exon 7) of the RNF130 gene. This alteration results from a C to G substitution at nucleotide position 1060, causing the leucine (L) at amino acid position 354 to be replaced by a valine (V). 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