NM_024411.5:c.-20+3296T>C

Variant names:

• chr20-1989288-A-G
• rs2235751
• NM_024411.5:c.-20+3296T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024411.5(PDYN):​c.-20+3296T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,976 control chromosomes in the GnomAD database, including 14,937 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 0.40 (14937 hom., cov: 32)
• Consequence: PDYN NM_024411.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 19 publications found

Genes affected

PDYN (HGNC:8820): (prodynorphin) The protein encoded by this gene is a preproprotein that is proteolytically processed to form the secreted opioid peptides beta-neoendorphin, dynorphin, leu-enkephalin, rimorphin, and leumorphin. These peptides are ligands for the kappa-type of opioid receptor. Dynorphin is involved in modulating responses to several psychoactive substances, including cocaine. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]

PDYN-AS1 (HGNC:53462): (PDYN antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024411.5. 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
	PDYN	NM_024411.5	MANE Select	c.-20+3296T>C		intron	N/A	NP_077722.1
	PDYN	NM_001190892.1		c.-20+3296T>C		intron	N/A	NP_001177821.1
	PDYN	NM_001190898.3		c.-17+3296T>C		intron	N/A	NP_001177827.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN	ENST00000217305.3	TSL:1 MANE Select	c.-20+3296T>C		intron	N/A	ENSP00000217305.2
	PDYN	ENST00000539905.5	TSL:4	c.-20+4623T>C		intron	N/A	ENSP00000440185.1
	PDYN	ENST00000540134.5	TSL:4	c.-20+3296T>C		intron	N/A	ENSP00000442259.1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60692 AN: 151858 Hom.: 14918 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.351

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.400 AC: 60773 AN: 151976 Hom.: 14937 Cov.: 32 AF XY: 0.404 AC XY: 29990 AN XY: 74286

African (AFR) AF: 0.653 AC: 27051 AN: 41436

American (AMR) AF: 0.333 AC: 5078 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 925 AN: 3472

East Asian (EAS) AF: 0.841 AC: 4340 AN: 5160

South Asian (SAS) AF: 0.488 AC: 2347 AN: 4812

European-Finnish (FIN) AF: 0.293 AC: 3093 AN: 10570

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16832 AN: 67948

Other (OTH) AF: 0.357 AC: 752 AN: 2106

Alfa AF: 0.301 Hom.: 36531

Bravo AF: 0.412

Asia WGS AF: 0.691 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

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: rs2235751; hg19: chr20-1969934;