1-170166709-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001136107.2(NTMT2):c.538C>T(p.Pro180Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000902 in 1,552,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P180H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001136107.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTMT2 | NM_001136107.2 | c.538C>T | p.Pro180Ser | missense_variant | Exon 3 of 4 | ENST00000439373.3 | NP_001129579.1 | |
NTMT2 | XM_011509232.3 | c.343C>T | p.Pro115Ser | missense_variant | Exon 4 of 5 | XP_011507534.1 | ||
NTMT2 | XM_011509233.3 | c.343C>T | p.Pro115Ser | missense_variant | Exon 5 of 6 | XP_011507535.1 | ||
NTMT2 | XM_011509234.3 | c.343C>T | p.Pro115Ser | missense_variant | Exon 4 of 5 | XP_011507536.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152142Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000571 AC: 8AN: 1400012Hom.: 0 Cov.: 33 AF XY: 0.00000290 AC XY: 2AN XY: 690476
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.538C>T (p.P180S) alteration is located in exon 3 (coding exon 3) of the METTL11B gene. This alteration results from a C to T substitution at nucleotide position 538, causing the proline (P) at amino acid position 180 to be replaced by a serine (S). 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