chr1-171783899-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015935.5(METTL13):āc.313A>Gā(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 (ā ). 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