rs878853178
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NR_003051.4(RMRP):n.4_5insGAAGCTGAGGACGTGGT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000275 in 690,820 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NR_003051.4 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RMRP | NR_003051.4 | n.4_5insGAAGCTGAGGACGTGGT | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RMRP | ENST00000363046.1 | n.2_3insGAAGCTGAGGACGTGGT | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000156 AC: 2AN: 128286Hom.: 0 AF XY: 0.0000285 AC XY: 2AN XY: 70056
GnomAD4 exome AF: 0.0000334 AC: 18AN: 538686Hom.: 0 Cov.: 0 AF XY: 0.0000276 AC XY: 8AN XY: 290162
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
Metaphyseal chondrodysplasia, McKusick type Pathogenic:1
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Anauxetic dysplasia Pathogenic:1
This variant occurs in the RMRP gene, which encodes an RNA molecule that does not result in a protein product. This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant has been observed in individual(s) with RMRP-related conditions (PMID: 14608646, 16832578). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.-15_2dup. Studies have shown that this variant alters RMRP gene expression (PMID: 17937437). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at