9-35658025-T-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The variant allele was found at a frequency of 0.0000146 in 687,280 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 0.000013 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000015 ( 0 hom. )
Scores
2
Clinical Significance
Conservation
PhyloP100: -11.8
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| use as main transcript | n.35658025T>A | intergenic_region | ||||||
| RMRP | NR_003051.4 | n.-6A>T | upstream_gene_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| RMRP | ENST00000363046.1 | n.-8A>T | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 34
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GnomAD4 exome AF: 0.0000149 AC: 8AN: 535124Hom.: 0 Cov.: 0 AF XY: 0.0000174 AC XY: 5AN XY: 287848
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GnomAD4 genome 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74356
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Metaphyseal chondrodysplasia, McKusick type Uncertain:1
| Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jul 02, 2020 | - - |
Anauxetic dysplasia Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 14, 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 affected with RMRP-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant 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
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at