rs882968
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000546688.1(MRPL2P1):n.575C>A 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 0.658 in 550,976 control chromosomes in the GnomAD database, including 123,216 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.67 ( 34276 hom., cov: 31)
Exomes 𝑓: 0.66 ( 88940 hom. )
Consequence
MRPL2P1
ENST00000546688.1 non_coding_transcript_exon
ENST00000546688.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.44
Genes affected
MRPL2P1 (HGNC:29698): (mitochondrial ribosomal protein L2 pseudogene 1)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC107984543 | XR_007063399.1 | n.170+36124C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL2P1 | ENST00000546688.1 | n.575C>A | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000651272.1 | n.359+36124C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.667 AC: 101266AN: 151840Hom.: 34247 Cov.: 31
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GnomAD4 exome AF: 0.655 AC: 261470AN: 399018Hom.: 88940 Cov.: 4 AF XY: 0.671 AC XY: 145752AN XY: 217148
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GnomAD4 genome ? AF: 0.667 AC: 101340AN: 151958Hom.: 34276 Cov.: 31 AF XY: 0.662 AC XY: 49189AN XY: 74256
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at