12-120534953-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014868.5(RNF10):c.142T>G(p.Ser48Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000288 in 1,599,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014868.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.142T>G | p.Ser48Ala | missense_variant | Exon 1 of 17 | ENST00000325954.9 | NP_055683.3 | |
RNF10 | NM_001330474.2 | c.142T>G | p.Ser48Ala | missense_variant | Exon 1 of 17 | NP_001317403.1 | ||
LOC128071547 | NM_001414895.1 | c.257T>G | p.Val86Gly | missense_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.142T>G | p.Ser48Ala | missense_variant | Exon 1 of 17 | 1 | NM_014868.5 | ENSP00000322242.4 | ||
ENSG00000288623 | ENST00000675818.1 | c.257T>G | p.Val86Gly | missense_variant | Exon 1 of 1 | ENSP00000502390.1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000718 AC: 16AN: 222958Hom.: 1 AF XY: 0.0000806 AC XY: 10AN XY: 124022
GnomAD4 exome AF: 0.0000276 AC: 40AN: 1447450Hom.: 0 Cov.: 31 AF XY: 0.0000430 AC XY: 31AN XY: 720460
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.142T>G (p.S48A) alteration is located in exon 1 (coding exon 1) of the RNF10 gene. This alteration results from a T to G substitution at nucleotide position 142, causing the serine (S) at amino acid position 48 to be replaced by an alanine (A). 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