13-102694458-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001010977.3(METTL21C):c.41G>A(p.Arg14Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000747 in 1,458,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001010977.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL21C | NM_001010977.3 | c.41G>A | p.Arg14Gln | missense_variant | 1/4 | ENST00000267273.7 | |
METTL21C | XM_047430117.1 | c.41G>A | p.Arg14Gln | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL21C | ENST00000267273.7 | c.41G>A | p.Arg14Gln | missense_variant | 1/4 | 1 | NM_001010977.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00121 AC: 6AN: 4976Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.0000370 AC: 9AN: 243234Hom.: 0 AF XY: 0.0000378 AC XY: 5AN XY: 132128
GnomAD4 exome AF: 0.0000709 AC: 103AN: 1453610Hom.: 0 Cov.: 33 AF XY: 0.0000664 AC XY: 48AN XY: 723316
GnomAD4 genome AF: 0.00121 AC: 6AN: 4976Hom.: 0 Cov.: 0 AF XY: 0.00248 AC XY: 6AN XY: 2416
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at