rs4646337

Variant names:

• chr11-114312587-A-C
• rs4646337
• NM_006169.3:c.*110A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-114312587-A-C
• chr11-114312587-A-G
• chr11-114312587-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006169.3(NNMT):​c.*110A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NNMT NM_006169.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.47
• Publications: 7 publications found

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]

ENSG00000256947 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NNMT	NM_006169.3	c.*110A>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000299964.4	NP_006160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NNMT	ENST00000299964.4	c.*110A>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_006169.3	ENSP00000299964.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 914522 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 464574

African (AFR) AF: 0.00 AC: 0 AN: 22276

American (AMR) AF: 0.00 AC: 0 AN: 32354

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17894

East Asian (EAS) AF: 0.00 AC: 0 AN: 36834

South Asian (SAS) AF: 0.00 AC: 0 AN: 63046

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35094

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3036

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 662154

Other (OTH) AF: 0.00 AC: 0 AN: 41834

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.033
DANN	Benign	0.58
PhyloP100		-3.5

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4646337; hg19: chr11-114183309;