X-47169411-CATGGACTACCGTTCAT-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_005676.5(RBM10):c.117_132delGGACTACCGTTCATAT(p.Met39IlefsTer90) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005676.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBM10 | NM_005676.5 | c.117_132delGGACTACCGTTCATAT | p.Met39IlefsTer90 | frameshift_variant | Exon 3 of 24 | ENST00000377604.8 | NP_005667.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBM10 | ENST00000377604.8 | c.117_132delGGACTACCGTTCATAT | p.Met39IlefsTer90 | frameshift_variant | Exon 3 of 24 | 1 | NM_005676.5 | ENSP00000366829.3 | ||
RBM10 | ENST00000329236.8 | c.312_327delGGACTACCGTTCATAT | p.Met104IlefsTer90 | frameshift_variant | Exon 3 of 24 | 1 | ENSP00000328848.8 | |||
RBM10 | ENST00000628161.2 | c.117_132delGGACTACCGTTCATAT | p.Met39IlefsTer41 | frameshift_variant | Exon 3 of 23 | 1 | ENSP00000486115.1 | |||
RBM10 | ENST00000345781.10 | c.117_132delGGACTACCGTTCATAT | p.Met39IlefsTer41 | frameshift_variant | Exon 3 of 23 | 2 | ENSP00000329659.6 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
TARP syndrome Pathogenic:1
This frameshifting variant in exon 3 of 24 introduces a premature stop codon and is therefore predicted to result in loss of normal protein function. It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. Based on the available evidence, the c.117_132del (p.Met39IlefsTer90) variant is classified as Likely Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at