3-9838183-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000383820.10(RPUSD3):c.865C>T(p.Arg289Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,611,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000383820.10 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPUSD3 | NM_173659.5 | c.865C>T | p.Arg289Cys | missense_variant | 9/9 | ENST00000383820.10 | NP_775930.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPUSD3 | ENST00000383820.10 | c.865C>T | p.Arg289Cys | missense_variant | 9/9 | 1 | NM_173659.5 | ENSP00000373331 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000765 AC: 19AN: 248396Hom.: 0 AF XY: 0.0000744 AC XY: 10AN XY: 134470
GnomAD4 exome AF: 0.000129 AC: 188AN: 1459734Hom.: 0 Cov.: 31 AF XY: 0.000138 AC XY: 100AN XY: 726156
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 24, 2023 | The c.889C>T (p.R297C) alteration is located in exon 9 (coding exon 9) of the RPUSD3 gene. This alteration results from a C to T substitution at nucleotide position 889, causing the arginine (R) at amino acid position 297 to be replaced by a cysteine (C). 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