chr13-102694437-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010977.3(METTL21C):c.62C>T(p.Pro21Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,463,900 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_001010977.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL21C | NM_001010977.3 | c.62C>T | p.Pro21Leu | missense_variant | 1/4 | ENST00000267273.7 | |
METTL21C | XM_047430117.1 | c.62C>T | p.Pro21Leu | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL21C | ENST00000267273.7 | c.62C>T | p.Pro21Leu | missense_variant | 1/4 | 1 | NM_001010977.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000265 AC: 2AN: 7560Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246974Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133852
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1456340Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 724640
GnomAD4 genome AF: 0.000265 AC: 2AN: 7560Hom.: 0 Cov.: 0 AF XY: 0.000266 AC XY: 1AN XY: 3764
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at