rs5638

chr17-39669996-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_002686.4(PNMT):c.456A>G(p.Lys152=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 1,603,634 control chromosomes in the GnomAD database, including 1,159 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 0.057 (473 hom., cov: 32)
  • Exomes 𝑓: 0.020 (686 hom.)
• Consequence: PNMT NM_002686.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP7: Synonymous conserved (PhyloP=2.01 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNMT	NM_002686.4	c.456A>G	p.Lys152=	synonymous_variant	3/3	ENST00000269582.3
PNMT	XM_011524909.3	c.162A>G	p.Lys54=	synonymous_variant	3/3
PNMT	NR_073461.2	n.306A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNMT	ENST00000269582.3	c.456A>G	p.Lys152=	synonymous_variant	3/3	1	NM_002686.4	P1
PNMT	ENST00000394246.1	c.162A>G	p.Lys54=	synonymous_variant	3/3	2
PNMT	ENST00000581428.1	c.*156A>G		3_prime_UTR_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8576 AN: 151926 Hom.: 472 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0321

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0378

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0421

GnomAD3 exomes AF: 0.0283 AC: 6865 AN: 242458 Hom.: 244 AF XY: 0.0264 AC XY: 3491 AN XY: 131996

Gnomad AFR exome AF: 0.143

Gnomad AMR exome AF: 0.0158

Gnomad ASJ exome AF: 0.0184

Gnomad EAS exome AF: 0.00121

Gnomad SAS exome AF: 0.0356

Gnomad FIN exome AF: 0.0278

Gnomad NFE exome AF: 0.0193

Gnomad OTH exome AF: 0.0243

GnomAD4 exome AF: 0.0202 AC: 29307 AN: 1451590 Hom.: 686 Cov.: 32 AF XY: 0.0206 AC XY: 14881 AN XY: 722300

Gnomad4 AFR exome AF: 0.139

Gnomad4 AMR exome AF: 0.0161

Gnomad4 ASJ exome AF: 0.0190

Gnomad4 EAS exome AF: 0.000555

Gnomad4 SAS exome AF: 0.0341

Gnomad4 FIN exome AF: 0.0288

Gnomad4 NFE exome AF: 0.0155

Gnomad4 OTH exome AF: 0.0283

GnomAD4 genome AF: 0.0566 AC: 8605 AN: 152044 Hom.: 473 Cov.: 32 AF XY: 0.0564 AC XY: 4192 AN XY: 74318

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0321

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0374

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0262 Hom.: 201

Bravo AF: 0.0585

Asia WGS AF: 0.0330 AC: 117 AN: 3478

EpiCase AF: 0.0220

EpiControl AF: 0.0204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	9.9
Dann	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs5638; hg19: chr17-37826249;