12-120534842-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014868.5(RNF10):āc.31A>Gā(p.Thr11Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,602,846 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 (ā ).
Frequency
Consequence
NM_014868.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF10 | NM_014868.5 | c.31A>G | p.Thr11Ala | missense_variant | 1/17 | ENST00000325954.9 | |
LOC128071547 | NM_001414895.1 | c.146A>G | p.His49Arg | missense_variant | 1/1 | ENST00000675818.1 | |
RNF10 | NM_001330474.2 | c.31A>G | p.Thr11Ala | missense_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF10 | ENST00000325954.9 | c.31A>G | p.Thr11Ala | missense_variant | 1/17 | 1 | NM_014868.5 | P1 | |
ENST00000675818.1 | c.146A>G | p.His49Arg | missense_variant | 1/1 | NM_001414895.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 151932Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000660 AC: 15AN: 227382Hom.: 0 AF XY: 0.0000398 AC XY: 5AN XY: 125582
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1450914Hom.: 0 Cov.: 31 AF XY: 0.00000831 AC XY: 6AN XY: 721904
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 151932Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74214
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.31A>G (p.T11A) alteration is located in exon 1 (coding exon 1) of the RNF10 gene. This alteration results from a A to G substitution at nucleotide position 31, causing the threonine (T) at amino acid position 11 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