11-126203512-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032795.3(RPUSD4):c.1040G>A(p.Arg347His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R347C) has been classified as Uncertain significance.
Frequency
Consequence
NM_032795.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPUSD4 | NM_032795.3 | c.1040G>A | p.Arg347His | missense_variant | 7/7 | ENST00000298317.9 | |
RPUSD4 | NM_001363516.2 | c.1037G>A | p.Arg346His | missense_variant | 7/7 | ||
RPUSD4 | NM_001144827.2 | c.947G>A | p.Arg316His | missense_variant | 7/7 | ||
RPUSD4 | XM_011543039.3 | c.461G>A | p.Arg154His | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPUSD4 | ENST00000298317.9 | c.1040G>A | p.Arg347His | missense_variant | 7/7 | 1 | NM_032795.3 | P1 | |
RPUSD4 | ENST00000533628.5 | c.947G>A | p.Arg316His | missense_variant | 7/7 | 1 | |||
RPUSD4 | ENST00000526942.5 | n.1061G>A | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
RPUSD4 | ENST00000530903.1 | n.1214G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251438Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135906
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727246
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74310
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at