17-2420271-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The ENST00000263092.11(METTL16):c.1388C>A(p.Thr463Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000205 in 1,613,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000263092.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
METTL16 | NM_024086.4 | c.1388C>A | p.Thr463Lys | missense_variant | 10/10 | ENST00000263092.11 | NP_076991.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
METTL16 | ENST00000263092.11 | c.1388C>A | p.Thr463Lys | missense_variant | 10/10 | 1 | NM_024086.4 | ENSP00000263092 | P1 | |
METTL16 | ENST00000571669.6 | n.1393C>A | non_coding_transcript_exon_variant | 9/9 | 5 | |||||
METTL16 | ENST00000574752.5 | c.*932C>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/10 | 5 | ENSP00000460207 | ||||
METTL16 | ENST00000576556.5 | c.*765C>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 2 | ENSP00000460775 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000803 AC: 20AN: 249000Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135176
GnomAD4 exome AF: 0.000212 AC: 310AN: 1461462Hom.: 0 Cov.: 31 AF XY: 0.000177 AC XY: 129AN XY: 727062
GnomAD4 genome AF: 0.000131 AC: 20AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.1388C>A (p.T463K) alteration is located in exon 10 (coding exon 9) of the METTL16 gene. This alteration results from a C to A substitution at nucleotide position 1388, causing the threonine (T) at amino acid position 463 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at