1-171783899-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015935.5(METTL13):c.313A>G(p.Met105Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,613,946 control chromosomes in the GnomAD database, including 65,318 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_015935.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL13 | NM_015935.5 | c.313A>G | p.Met105Val | missense_variant | 2/8 | ENST00000361735.4 | |
METTL13 | NM_014955.3 | c.55A>G | p.Met19Val | missense_variant | 2/8 | ||
METTL13 | NM_001007239.2 | c.313A>G | p.Met105Val | missense_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL13 | ENST00000361735.4 | c.313A>G | p.Met105Val | missense_variant | 2/8 | 1 | NM_015935.5 | P1 | |
METTL13 | ENST00000367737.9 | c.313A>G | p.Met105Val | missense_variant | 2/8 | 1 | |||
METTL13 | ENST00000362019.7 | c.55A>G | p.Met19Val | missense_variant | 2/8 | 2 | |||
METTL13 | ENST00000485629.1 | n.425A>G | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.294 AC: 44709AN: 151938Hom.: 6716 Cov.: 32
GnomAD3 exomes AF: 0.288 AC: 72392AN: 251452Hom.: 11318 AF XY: 0.282 AC XY: 38277AN XY: 135894
GnomAD4 exome AF: 0.277 AC: 405133AN: 1461890Hom.: 58598 Cov.: 50 AF XY: 0.275 AC XY: 200001AN XY: 727246
GnomAD4 genome ? AF: 0.294 AC: 44738AN: 152056Hom.: 6720 Cov.: 32 AF XY: 0.296 AC XY: 21992AN XY: 74316
ClinVar
Submissions by phenotype
METTL13-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at