11-126205758-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032795.3(RPUSD4):āc.581T>Cā(p.Met194Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000608 in 1,610,818 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 Uncertain significance (ā ).
Frequency
Consequence
NM_032795.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPUSD4 | NM_032795.3 | c.581T>C | p.Met194Thr | missense_variant | 4/7 | ENST00000298317.9 | |
RPUSD4 | XM_011543039.3 | c.2T>C | p.Met1? | start_lost | 2/5 | ||
RPUSD4 | NM_001363516.2 | c.581T>C | p.Met194Thr | missense_variant | 4/7 | ||
RPUSD4 | NM_001144827.2 | c.581T>C | p.Met194Thr | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPUSD4 | ENST00000298317.9 | c.581T>C | p.Met194Thr | missense_variant | 4/7 | 1 | NM_032795.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000113 AC: 28AN: 246934Hom.: 0 AF XY: 0.000105 AC XY: 14AN XY: 133436
GnomAD4 exome AF: 0.0000624 AC: 91AN: 1458592Hom.: 0 Cov.: 31 AF XY: 0.0000621 AC XY: 45AN XY: 725146
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2021 | The c.581T>C (p.M194T) alteration is located in exon 4 (coding exon 4) of the RPUSD4 gene. This alteration results from a T to C substitution at nucleotide position 581, causing the methionine (M) at amino acid position 194 to be replaced by a threonine (T). 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