rs1050900
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006895.3(HNMT):c.*218A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 423,498 control chromosomes in the GnomAD database, including 10,599 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 0.21 ( 3735 hom., cov: 32)
Exomes 𝑓: 0.22 ( 6864 hom. )
Consequence
HNMT
NM_006895.3 3_prime_UTR
NM_006895.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.187
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]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNMT | NM_006895.3 | c.*218A>T | 3_prime_UTR_variant | 6/6 | ENST00000280097.5 | ||
LOC107985948 | XR_001739719.2 | n.239-6552T>A | intron_variant, non_coding_transcript_variant | ||||
HNMT | XM_011511064.3 | c.*218A>T | 3_prime_UTR_variant | 5/5 | |||
HNMT | XM_017003948.2 | c.*218A>T | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNMT | ENST00000280097.5 | c.*218A>T | 3_prime_UTR_variant | 6/6 | 1 | NM_006895.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.213 AC: 32339AN: 151912Hom.: 3732 Cov.: 32
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GnomAD4 exome AF: 0.219 AC: 59385AN: 271468Hom.: 6864 Cov.: 0 AF XY: 0.221 AC XY: 30674AN XY: 138720
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GnomAD4 genome ? AF: 0.213 AC: 32369AN: 152030Hom.: 3735 Cov.: 32 AF XY: 0.218 AC XY: 16161AN XY: 74302
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at