chr11-114262912-G-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000535401.5(NNMT):c.-152G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,122 control chromosomes in the GnomAD database, including 6,201 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.27 ( 6199 hom., cov: 32)
Exomes 𝑓: 0.26 ( 2 hom. )
Consequence
NNMT
ENST00000535401.5 5_prime_UTR
ENST00000535401.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.620
Genes affected
NNMT (HGNC:7861): (nicotinamide N-methyltransferase) N-methylation is one method by which drug and other xenobiotic compounds are metabolized by the liver. This gene encodes the protein responsible for this enzymatic activity which uses S-adenosyl methionine as the methyl donor. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NNMT | NM_001372047.1 | c.-152G>T | 5_prime_UTR_variant | 2/5 | |||
NNMT | NR_164073.1 | n.351G>T | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NNMT | ENST00000535401.5 | c.-152G>T | 5_prime_UTR_variant | 2/5 | 1 | P1 | |||
ENST00000544925.1 | n.56+6572C>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
NNMT | ENST00000535185.5 | n.157G>T | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
NNMT | ENST00000541090.1 | n.25G>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.267 AC: 40616AN: 151958Hom.: 6182 Cov.: 32
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GnomAD4 exome AF: 0.261 AC: 12AN: 46Hom.: 2 Cov.: 0 AF XY: 0.289 AC XY: 11AN XY: 38
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GnomAD4 genome AF: 0.267 AC: 40671AN: 152076Hom.: 6199 Cov.: 32 AF XY: 0.276 AC XY: 20508AN XY: 74334
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at