11-28496555-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000532947.2(METTL15):c.*425-29923T>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0071 in 152,310 control chromosomes in the GnomAD database, including 8 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 0.0071 ( 8 hom., cov: 33)
Consequence
METTL15
ENST00000532947.2 intron, NMD_transcript
ENST00000532947.2 intron, NMD_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.135
Genes affected
METTL15 (HGNC:26606): (methyltransferase 15, mitochondrial 12S rRNA N4-cytidine) Predicted to enable rRNA (cytosine-N4-)-methyltransferase activity. Predicted to be involved in rRNA base methylation. Predicted to be located in mitochondrial matrix. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.91).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0071 (1081/152310) while in subpopulation AFR AF= 0.0236 (981/41552). AF 95% confidence interval is 0.0224. There are 8 homozygotes in gnomad4. There are 516 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL15 | XR_007062458.1 | n.1414-29923T>C | intron_variant, non_coding_transcript_variant | ||||
METTL15 | XR_930849.3 | n.1332-29923T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL15 | ENST00000532947.2 | c.*425-29923T>C | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00705 AC: 1073AN: 152192Hom.: 8 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00710 AC: 1081AN: 152310Hom.: 8 Cov.: 33 AF XY: 0.00693 AC XY: 516AN XY: 74502
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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