1-170160575-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001136107.2(NTMT2):āc.212G>Cā(p.Arg71Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000909 in 1,551,494 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000046 ( 0 hom., cov: 32)
Exomes š: 0.000096 ( 0 hom. )
Consequence
NTMT2
NM_001136107.2 missense
NM_001136107.2 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 9.05
Genes affected
NTMT2 (HGNC:31932): (N-terminal Xaa-Pro-Lys N-methyltransferase 2) Enables N-terminal protein N-methyltransferase activity. Involved in N-terminal protein amino acid methylation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTMT2 | NM_001136107.2 | c.212G>C | p.Arg71Thr | missense_variant | 2/4 | ENST00000439373.3 | NP_001129579.1 | |
NTMT2 | XM_011509232.3 | c.17G>C | p.Arg6Thr | missense_variant | 3/5 | XP_011507534.1 | ||
NTMT2 | XM_011509233.3 | c.17G>C | p.Arg6Thr | missense_variant | 4/6 | XP_011507535.1 | ||
NTMT2 | XM_011509234.3 | c.17G>C | p.Arg6Thr | missense_variant | 3/5 | XP_011507536.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTMT2 | ENST00000439373.3 | c.212G>C | p.Arg71Thr | missense_variant | 2/4 | 1 | NM_001136107.2 | ENSP00000408058 | P1 | |
NTMT2 | ENST00000367764.3 | n.207G>C | non_coding_transcript_exon_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000509 AC: 8AN: 157300Hom.: 0 AF XY: 0.0000361 AC XY: 3AN XY: 83156
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GnomAD4 exome AF: 0.0000958 AC: 134AN: 1399322Hom.: 0 Cov.: 31 AF XY: 0.000103 AC XY: 71AN XY: 690134
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.212G>C (p.R71T) alteration is located in exon 2 (coding exon 2) of the METTL11B gene. This alteration results from a G to C substitution at nucleotide position 212, causing the arginine (R) at amino acid position 71 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at