7-73840462-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152559.3(METTL27):c.340C>T(p.Arg114Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000287 in 1,604,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152559.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
METTL27 | NM_152559.3 | c.340C>T | p.Arg114Cys | missense_variant | Exon 4 of 6 | ENST00000297873.9 | NP_689772.2 | |
METTL27 | XM_017011777.2 | c.340C>T | p.Arg114Cys | missense_variant | Exon 4 of 6 | XP_016867266.1 | ||
METTL27 | XM_017011778.2 | c.340C>T | p.Arg114Cys | missense_variant | Exon 4 of 6 | XP_016867267.1 | ||
METTL27 | XR_001744563.2 | n.371C>T | non_coding_transcript_exon_variant | Exon 4 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
METTL27 | ENST00000297873.9 | c.340C>T | p.Arg114Cys | missense_variant | Exon 4 of 6 | 1 | NM_152559.3 | ENSP00000297873.4 | ||
METTL27 | ENST00000458679.5 | n.253-342C>T | intron_variant | Intron 3 of 4 | 4 | ENSP00000398533.1 | ||||
METTL27 | ENST00000493174.1 | n.284-342C>T | intron_variant | Intron 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152014Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000114 AC: 26AN: 228378Hom.: 0 AF XY: 0.000104 AC XY: 13AN XY: 125234
GnomAD4 exome AF: 0.0000296 AC: 43AN: 1452826Hom.: 0 Cov.: 31 AF XY: 0.0000332 AC XY: 24AN XY: 722208
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152014Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74240
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.340C>T (p.R114C) alteration is located in exon 4 (coding exon 3) of the WBSCR27 gene. This alteration results from a C to T substitution at nucleotide position 340, causing the arginine (R) at amino acid position 114 to be replaced by a cysteine (C). 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