chr1-171783958-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015935.5(METTL13):c.372G>C(p.Leu124=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
METTL13
NM_015935.5 synonymous
NM_015935.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.13
Genes affected
METTL13 (HGNC:24248): (methyltransferase 13, eEF1A N-terminus and K55) Predicted to enable methyltransferase activity. Involved in negative regulation of cell cycle G1/S phase transition and negative regulation of transcription by RNA polymerase II. Predicted to be located in mitochondrion 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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 1-171783958-G-C is Benign according to our data. Variant chr1-171783958-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3035848.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.13 with no splicing effect.
BS2
?
High AC in GnomAdExome at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL13 | NM_015935.5 | c.372G>C | p.Leu124= | synonymous_variant | 2/8 | ENST00000361735.4 | |
METTL13 | NM_014955.3 | c.114G>C | p.Leu38= | synonymous_variant | 2/8 | ||
METTL13 | NM_001007239.2 | c.372G>C | p.Leu124= | synonymous_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL13 | ENST00000361735.4 | c.372G>C | p.Leu124= | synonymous_variant | 2/8 | 1 | NM_015935.5 | P1 | |
METTL13 | ENST00000367737.9 | c.372G>C | p.Leu124= | synonymous_variant | 2/8 | 1 | |||
METTL13 | ENST00000362019.7 | c.114G>C | p.Leu38= | synonymous_variant | 2/8 | 2 | |||
METTL13 | ENST00000485629.1 | n.484G>C | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251478Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135920
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461894Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 727248
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74498
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
METTL13-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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