11-126203513-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032795.3(RPUSD4):c.1039C>T(p.Arg347Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,614,068 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 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. R347H) has been classified as Likely benign.
Frequency
Consequence
NM_032795.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPUSD4 | NM_032795.3 | c.1039C>T | p.Arg347Cys | missense_variant | 7/7 | ENST00000298317.9 | |
RPUSD4 | NM_001363516.2 | c.1036C>T | p.Arg346Cys | missense_variant | 7/7 | ||
RPUSD4 | NM_001144827.2 | c.946C>T | p.Arg316Cys | missense_variant | 7/7 | ||
RPUSD4 | XM_011543039.3 | c.460C>T | p.Arg154Cys | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPUSD4 | ENST00000298317.9 | c.1039C>T | p.Arg347Cys | missense_variant | 7/7 | 1 | NM_032795.3 | P1 | |
RPUSD4 | ENST00000533628.5 | c.946C>T | p.Arg316Cys | missense_variant | 7/7 | 1 | |||
RPUSD4 | ENST00000526942.5 | n.1060C>T | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
RPUSD4 | ENST00000530903.1 | n.1213C>T | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251434Hom.: 1 AF XY: 0.0000736 AC XY: 10AN XY: 135900
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461888Hom.: 1 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727246
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.1039C>T (p.R347C) alteration is located in exon 7 (coding exon 7) of the RPUSD4 gene. This alteration results from a C to T substitution at nucleotide position 1039, causing the arginine (R) at amino acid position 347 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