chr13-102686144-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010977.3(METTL21C):āc.682A>Gā(p.Ser228Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,614,090 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (ā ).
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.682A>G | p.Ser228Gly | missense_variant | 4/4 | ENST00000267273.7 | |
METTL21C | XM_047430117.1 | c.682A>G | p.Ser228Gly | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL21C | ENST00000267273.7 | c.682A>G | p.Ser228Gly | missense_variant | 4/4 | 1 | NM_001010977.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152236Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000346 AC: 87AN: 251322Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135826
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.000179 AC XY: 130AN XY: 727224
GnomAD4 genome AF: 0.000204 AC: 31AN: 152236Hom.: 1 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.682A>G (p.S228G) alteration is located in exon 4 (coding exon 4) of the METTL21C gene. This alteration results from a A to G substitution at nucleotide position 682, causing the serine (S) at amino acid position 228 to be replaced by a glycine (G). 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