rs759632477
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NR_003051.4(RMRP):n.146C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0000591 in 694,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000061 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000059 ( 0 hom. )
Consequence
RMRP
NR_003051.4 non_coding_transcript_exon
NR_003051.4 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.67
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RMRP | NR_003051.4 | n.146C>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RMRP | ENST00000363046.1 | n.144C>T | non_coding_transcript_exon_variant | 1/1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000611 AC: 9AN: 147410Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000766 AC: 10AN: 130490Hom.: 0 AF XY: 0.000126 AC XY: 9AN XY: 71222
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GnomAD4 exome AF: 0.0000585 AC: 32AN: 546738Hom.: 0 Cov.: 0 AF XY: 0.0000574 AC XY: 17AN XY: 296176
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GnomAD4 genome AF: 0.0000611 AC: 9AN: 147410Hom.: 0 Cov.: 34 AF XY: 0.0000833 AC XY: 6AN XY: 72060
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Metaphyseal chondrodysplasia, McKusick type Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 02, 2018 | - - |
Anauxetic dysplasia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 22, 2021 | This variant occurs in the RMRP gene, which encodes an RNA molecule that does not result in a protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals with RMRP-related conditions. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of this non-coding change is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at