chr1-171784135-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015935.5(METTL13):c.549G>A(p.Val183=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000231 in 1,614,252 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00013 ( 1 hom. )
Consequence
METTL13
NM_015935.5 synonymous
NM_015935.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0930
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=-0.5).
BP6
Variant 1-171784135-G-A is Benign according to our data. Variant chr1-171784135-G-A is described in ClinVar as [Benign]. Clinvar id is 3042833.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.093 with no splicing effect.
BS2
High AC in GnomAd4 at 181 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL13 | NM_015935.5 | c.549G>A | p.Val183= | synonymous_variant | 2/8 | ENST00000361735.4 | |
METTL13 | NM_014955.3 | c.291G>A | p.Val97= | synonymous_variant | 2/8 | ||
METTL13 | NM_001007239.2 | c.453+96G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL13 | ENST00000361735.4 | c.549G>A | p.Val183= | synonymous_variant | 2/8 | 1 | NM_015935.5 | P1 | |
METTL13 | ENST00000367737.9 | c.453+96G>A | intron_variant | 1 | |||||
METTL13 | ENST00000362019.7 | c.291G>A | p.Val97= | synonymous_variant | 2/8 | 2 | |||
METTL13 | ENST00000485629.1 | n.565+96G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00116 AC: 177AN: 152260Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000310 AC: 78AN: 251304Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135844
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GnomAD4 exome AF: 0.000131 AC: 192AN: 1461874Hom.: 1 Cov.: 35 AF XY: 0.000114 AC XY: 83AN XY: 727238
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GnomAD4 genome AF: 0.00119 AC: 181AN: 152378Hom.: 1 Cov.: 33 AF XY: 0.00123 AC XY: 92AN XY: 74504
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
METTL13-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 22, 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at