rs11871981
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024086.4(METTL16):c.729-10664T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 152,198 control chromosomes in the GnomAD database, including 448 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 0.065 ( 448 hom., cov: 32)
Consequence
METTL16
NM_024086.4 intron
NM_024086.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.147
Genes affected
METTL16 (HGNC:28484): (methyltransferase 16, RNA N6-adenosine) Enables RNA binding activity and RNA methyltransferase activity. Involved in RNA modification and regulation of mRNA metabolic process. Located in cytoplasm and nucleus. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0989 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL16 | NM_024086.4 | c.729-10664T>G | intron_variant | ENST00000263092.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL16 | ENST00000263092.11 | c.729-10664T>G | intron_variant | 1 | NM_024086.4 | P1 | |||
METTL16 | ENST00000574752.5 | c.*106-10664T>G | intron_variant, NMD_transcript_variant | 5 | |||||
METTL16 | ENST00000576556.5 | c.*106-10664T>G | intron_variant, NMD_transcript_variant | 2 | |||||
METTL16 | ENST00000571669.6 | n.734-10664T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0654 AC: 9941AN: 152086Hom.: 448 Cov.: 32
GnomAD3 genomes
?
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9941
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152086
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0653 AC: 9939AN: 152198Hom.: 448 Cov.: 32 AF XY: 0.0620 AC XY: 4616AN XY: 74414
GnomAD4 genome
?
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AC:
9939
AN:
152198
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32
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4616
AN XY:
74414
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68
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at