rs6442522
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000443029.5(METTL6):c.*11+12196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,894 control chromosomes in the GnomAD database, including 21,809 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 0.53 ( 21809 hom., cov: 30)
Consequence
METTL6
ENST00000443029.5 intron
ENST00000443029.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.921
Genes affected
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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=-0.97).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL6 | XM_005264867.5 | c.*11+12196G>A | intron_variant | ||||
METTL6 | XM_006712972.5 | c.618-14862G>A | intron_variant | ||||
METTL6 | XM_017005719.2 | c.*11+12196G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL6 | ENST00000443029.5 | c.*11+12196G>A | intron_variant | 5 | P1 | ||||
METTL6 | ENST00000458728.5 | c.279-14862G>A | intron_variant | 3 | |||||
METTL6 | ENST00000584799.1 | n.104+339G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.527 AC: 80012AN: 151774Hom.: 21763 Cov.: 30
GnomAD3 genomes
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80012
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.527 AC: 80118AN: 151894Hom.: 21809 Cov.: 30 AF XY: 0.523 AC XY: 38804AN XY: 74200
GnomAD4 genome
?
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AC:
80118
AN:
151894
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30
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38804
AN XY:
74200
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Asia WGS
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1754
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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