rs200173
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002686.4(PNMT):c.202+159A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.99 in 152,132 control chromosomes in the GnomAD database, including 74,627 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 0.99 ( 74627 hom., cov: 28)
Consequence
PNMT
NM_002686.4 intron
NM_002686.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.675
Genes affected
PNMT (HGNC:9160): (phenylethanolamine N-methyltransferase) The product of this gene catalyzes the last step of the catecholamine biosynthesis pathway, which methylates norepinephrine to form epinephrine (adrenaline). The enzyme also has beta-carboline 2N-methyltransferase activity. This gene is thought to play a key step in regulating epinephrine production. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2012]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNMT | NM_002686.4 | c.202+159A>G | intron_variant | ENST00000269582.3 | |||
PNMT | XM_011524909.3 | c.-278A>G | 5_prime_UTR_variant | 1/3 | |||
PNMT | NR_073461.2 | n.52+766A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNMT | ENST00000269582.3 | c.202+159A>G | intron_variant | 1 | NM_002686.4 | P1 | |||
PNMT | ENST00000394246.1 | c.-93+766A>G | intron_variant | 2 | |||||
PNMT | ENST00000581428.1 | c.202+159A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.990 AC: 150561AN: 152014Hom.: 74568 Cov.: 28
GnomAD3 genomes
?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.990 AC: 150679AN: 152132Hom.: 74627 Cov.: 28 AF XY: 0.991 AC XY: 73692AN XY: 74364
GnomAD4 genome
?
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150679
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152132
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28
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73692
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74364
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3472
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at