chr1-171784414-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015935.5(METTL13):c.828C>A(p.Asp276Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000324 in 1,542,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015935.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL13 | NM_015935.5 | c.828C>A | p.Asp276Glu | missense_variant | 2/8 | ENST00000361735.4 | |
METTL13 | NM_014955.3 | c.570C>A | p.Asp190Glu | missense_variant | 2/8 | ||
METTL13 | NM_001007239.2 | c.453+375C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL13 | ENST00000361735.4 | c.828C>A | p.Asp276Glu | missense_variant | 2/8 | 1 | NM_015935.5 | P1 | |
METTL13 | ENST00000367737.9 | c.453+375C>A | intron_variant | 1 | |||||
METTL13 | ENST00000362019.7 | c.570C>A | p.Asp190Glu | missense_variant | 2/8 | 2 | |||
METTL13 | ENST00000485629.1 | n.565+375C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000108 AC: 2AN: 185928Hom.: 0 AF XY: 0.0000203 AC XY: 2AN XY: 98686
GnomAD4 exome AF: 0.00000216 AC: 3AN: 1390214Hom.: 0 Cov.: 34 AF XY: 0.00000292 AC XY: 2AN XY: 684062
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.828C>A (p.D276E) alteration is located in exon 2 (coding exon 2) of the METTL13 gene. This alteration results from a C to A substitution at nucleotide position 828, causing the aspartic acid (D) at amino acid position 276 to be replaced by a glutamic acid (E). 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