11-114312274-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006169.3(NNMT):c.592G>A(p.Ala198Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000496 in 1,614,118 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_006169.3 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NNMT | NM_006169.3 | c.592G>A | p.Ala198Thr | missense_variant | 3/3 | ENST00000299964.4 | NP_006160.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NNMT | ENST00000299964.4 | c.592G>A | p.Ala198Thr | missense_variant | 3/3 | 1 | NM_006169.3 | ENSP00000299964.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251378Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135864
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461890Hom.: 1 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727244
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2024 | The c.592G>A (p.A198T) alteration is located in exon 3 (coding exon 3) of the NNMT gene. This alteration results from a G to A substitution at nucleotide position 592, causing the alanine (A) at amino acid position 198 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