chr11-126203482-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032795.3(RPUSD4):c.1070G>A(p.Arg357His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,614,158 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 (★).
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.1070G>A | p.Arg357His | missense_variant | 7/7 | ENST00000298317.9 | |
RPUSD4 | NM_001363516.2 | c.1067G>A | p.Arg356His | missense_variant | 7/7 | ||
RPUSD4 | NM_001144827.2 | c.977G>A | p.Arg326His | missense_variant | 7/7 | ||
RPUSD4 | XM_011543039.3 | c.491G>A | p.Arg164His | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPUSD4 | ENST00000298317.9 | c.1070G>A | p.Arg357His | missense_variant | 7/7 | 1 | NM_032795.3 | P1 | |
RPUSD4 | ENST00000533628.5 | c.977G>A | p.Arg326His | missense_variant | 7/7 | 1 | |||
RPUSD4 | ENST00000526942.5 | n.1091G>A | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
RPUSD4 | ENST00000530903.1 | n.1244G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251424Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135884
GnomAD4 exome AF: 0.000122 AC: 179AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.000131 AC XY: 95AN XY: 727240
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.1070G>A (p.R357H) alteration is located in exon 7 (coding exon 7) of the RPUSD4 gene. This alteration results from a G to A substitution at nucleotide position 1070, causing the arginine (R) at amino acid position 357 to be replaced by a histidine (H). 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