13-102694443-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010977.3(METTL21C):c.56G>A(p.Ser19Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,216 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 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.56G>A | p.Ser19Asn | missense_variant | 1/4 | ENST00000267273.7 | |
METTL21C | XM_047430117.1 | c.56G>A | p.Ser19Asn | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL21C | ENST00000267273.7 | c.56G>A | p.Ser19Asn | missense_variant | 1/4 | 1 | NM_001010977.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 6550Hom.: 0 Cov.: 0 FAILED QC
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457216Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725114
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 6550Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 3198
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.56G>A (p.S19N) alteration is located in exon 1 (coding exon 1) of the METTL21C gene. This alteration results from a G to A substitution at nucleotide position 56, causing the serine (S) at amino acid position 19 to be replaced by an asparagine (N). 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