12-120534876-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_014868.5(RNF10):c.65A>G(p.Asn22Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 Likely benign (★).
Frequency
Consequence
NM_014868.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF10 | NM_014868.5 | c.65A>G | p.Asn22Ser | missense_variant | Exon 1 of 17 | ENST00000325954.9 | NP_055683.3 | |
RNF10 | NM_001330474.2 | c.65A>G | p.Asn22Ser | missense_variant | Exon 1 of 17 | NP_001317403.1 | ||
LOC128071547 | NM_001414895.1 | c.180A>G | p.Gln60Gln | synonymous_variant | Exon 1 of 1 | NP_001401824.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF10 | ENST00000325954.9 | c.65A>G | p.Asn22Ser | missense_variant | Exon 1 of 17 | 1 | NM_014868.5 | ENSP00000322242.4 | ||
ENSG00000288623 | ENST00000675818.1 | c.180A>G | p.Gln60Gln | synonymous_variant | Exon 1 of 1 | ENSP00000502390.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.