chr1-171784367-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015935.5(METTL13):c.781C>T(p.Arg261Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,574,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R261H) has been classified as Uncertain significance.
Frequency
Consequence
NM_015935.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL13 | NM_015935.5 | c.781C>T | p.Arg261Cys | missense_variant | 2/8 | ENST00000361735.4 | |
METTL13 | NM_014955.3 | c.523C>T | p.Arg175Cys | missense_variant | 2/8 | ||
METTL13 | NM_001007239.2 | c.453+328C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL13 | ENST00000361735.4 | c.781C>T | p.Arg261Cys | missense_variant | 2/8 | 1 | NM_015935.5 | P1 | |
METTL13 | ENST00000367737.9 | c.453+328C>T | intron_variant | 1 | |||||
METTL13 | ENST00000362019.7 | c.523C>T | p.Arg175Cys | missense_variant | 2/8 | 2 | |||
METTL13 | ENST00000485629.1 | n.565+328C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000651 AC: 14AN: 214972Hom.: 0 AF XY: 0.0000697 AC XY: 8AN XY: 114788
GnomAD4 exome AF: 0.0000274 AC: 39AN: 1422158Hom.: 0 Cov.: 34 AF XY: 0.0000327 AC XY: 23AN XY: 702820
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.781C>T (p.R261C) alteration is located in exon 2 (coding exon 2) of the METTL13 gene. This alteration results from a C to T substitution at nucleotide position 781, causing the arginine (R) at amino acid position 261 to be replaced by a cysteine (C). 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