17-39668292-G-T

Variant names:

• chr17-39668292-G-T
• rs876493
• ENST00000394246.1:c.-93+222G>T

Variant summary

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

The ENST00000394246.1(PNMT):​c.-93+222G>T variant causes a intron 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: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PNMT ENST00000394246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 0 publications found

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]

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=-0.69).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000394246.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNMT	NR_073461.2		n.52+222G>T		intron	N/A
	PNMT	NM_002686.4	MANE Select	c.-184G>T		upstream_gene	N/A	NP_002677.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNMT	ENST00000394246.1	TSL:2	c.-93+222G>T		intron	N/A	ENSP00000377791.1
	PNMT	ENST00000269582.3	TSL:1 MANE Select	c.-184G>T		upstream_gene	N/A	ENSP00000269582.2
	PNMT	ENST00000581428.1	TSL:2	c.-184G>T		upstream_gene	N/A	ENSP00000464234.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 315528 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 162642

African (AFR) AF: 0.00 AC: 0 AN: 7364

American (AMR) AF: 0.00 AC: 0 AN: 7222

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9912

East Asian (EAS) AF: 0.00 AC: 0 AN: 22170

South Asian (SAS) AF: 0.00 AC: 0 AN: 15782

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24946

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1516

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 207174

Other (OTH) AF: 0.00 AC: 0 AN: 19442

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		-0.17
PromoterAI		-0.052	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs876493; hg19: chr17-37824545;