NM_014868.5:c.142T>C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014868.5(RNF10):c.142T>C(p.Ser48Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000369 in 1,599,490 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S48A) has been classified as Uncertain significance.
Frequency
Consequence
NM_014868.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF10 | NM_014868.5 | c.142T>C | p.Ser48Pro | missense_variant | Exon 1 of 17 | ENST00000325954.9 | NP_055683.3 | |
RNF10 | NM_001330474.2 | c.142T>C | p.Ser48Pro | missense_variant | Exon 1 of 17 | NP_001317403.1 | ||
LOC128071547 | NM_001414895.1 | c.257T>C | p.Val86Ala | 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>C | p.Ser48Pro | missense_variant | Exon 1 of 17 | 1 | NM_014868.5 | ENSP00000322242.4 | ||
ENSG00000288623 | ENST00000675818.1 | c.257T>C | p.Val86Ala | missense_variant | Exon 1 of 1 | ENSP00000502390.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000314 AC: 7AN: 222958Hom.: 0 AF XY: 0.0000161 AC XY: 2AN XY: 124022
GnomAD4 exome AF: 0.0000401 AC: 58AN: 1447450Hom.: 0 Cov.: 31 AF XY: 0.0000347 AC XY: 25AN XY: 720460
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.142T>C (p.S48P) alteration is located in exon 1 (coding exon 1) of the RNF10 gene. This alteration results from a T to C substitution at nucleotide position 142, causing the serine (S) at amino acid position 48 to be replaced by a proline (P). 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