7-73834883-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152559.3(METTL27):c.598C>A(p.Pro200Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,613,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
METTL27 | NM_152559.3 | c.598C>A | p.Pro200Thr | missense_variant | Exon 6 of 6 | ENST00000297873.9 | NP_689772.2 | |
METTL27 | XM_017011777.2 | c.676C>A | p.Pro226Thr | missense_variant | Exon 6 of 6 | XP_016867266.1 | ||
METTL27 | XM_017011778.2 | c.676C>A | p.Pro226Thr | missense_variant | Exon 6 of 6 | XP_016867267.1 | ||
METTL27 | XR_001744563.2 | n.807C>A | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251194Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135830
GnomAD4 exome AF: 0.000248 AC: 363AN: 1461738Hom.: 0 Cov.: 89 AF XY: 0.000232 AC XY: 169AN XY: 727188
GnomAD4 genome AF: 0.000151 AC: 23AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.598C>A (p.P200T) alteration is located in exon 6 (coding exon 5) of the WBSCR27 gene. This alteration results from a C to A substitution at nucleotide position 598, causing the proline (P) at amino acid position 200 to be replaced by a threonine (T). 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