rs1455157

chr2-138016182-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006895.3(HNMT):c.*2052T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,038 control chromosomes in the GnomAD database, including 9,000 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 0.31 (9000 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: HNMT NM_006895.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

HNMT (HGNC:5028): (histamine N-methyltransferase) In mammals, histamine is metabolized by two major pathways: N(tau)-methylation via histamine N-methyltransferase and oxidative deamination via diamine oxidase. This gene encodes the first enzyme which is found in the cytosol and uses S-adenosyl-L-methionine as the methyl donor. In the mammalian brain, the neurotransmitter activity of histamine is controlled by N(tau)-methylation as diamine oxidase is not found in the central nervous system. A common genetic polymorphism affects the activity levels of this gene product in red blood cells. Multiple alternatively spliced transcript variants that encode different proteins have been found for this gene. [provided by RefSeq, Jul 2008]

LOC107985948 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNMT	NM_006895.3	c.*2052T>C		3_prime_UTR_variant	6/6	ENST00000280097.5
LOC107985948	XR_001739719.2	n.239-8386A>G		intron_variant, non_coding_transcript_variant
HNMT	XM_011511064.3	c.*2052T>C		3_prime_UTR_variant	5/5
HNMT	XM_017003948.2	c.*2052T>C		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNMT	ENST00000280097.5	c.*2052T>C		3_prime_UTR_variant	6/6	1	NM_006895.3	P1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47718 AN: 151916 Hom.: 8977 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.312

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.250

GnomAD4 genome AF: 0.314 AC: 47808 AN: 152034 Hom.: 9000 Cov.: 32 AF XY: 0.317 AC XY: 23526 AN XY: 74306

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.313

Alfa AF: 0.223 Hom.: 8215

Bravo AF: 0.329

Asia WGS AF: 0.351 AC: 1217 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455157; hg19: chr2-138773752;