20-2004404-G-A

Variant names:

• chr20-2004404-G-A
• rs2206699
• ENST00000446562.1:n.1217-2528G>A

Variant summary

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

The ENST00000446562.1(PDYN-AS1):​n.1217-2528G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,122 control chromosomes in the GnomAD database, including 44,988 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 0.77 (44988 hom., cov: 31)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.974
• Publications: 2 publications found

Genes affected

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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446562.1. 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
	PDYN-AS1	NR_134520.1		n.1253-2528G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.1217-2528G>A		intron	N/A
	PDYN-AS1	ENST00000651021.1		n.476-24196G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116393 AN: 152004 Hom.: 44942 Cov.: 31

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.766 AC: 116497 AN: 152122 Hom.: 44988 Cov.: 31 AF XY: 0.772 AC XY: 57387 AN XY: 74382

African (AFR) AF: 0.847 AC: 35140 AN: 41486

American (AMR) AF: 0.748 AC: 11446 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2414 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4431 AN: 5168

South Asian (SAS) AF: 0.850 AC: 4096 AN: 4818

European-Finnish (FIN) AF: 0.805 AC: 8515 AN: 10582

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48040 AN: 67980

Other (OTH) AF: 0.739 AC: 1558 AN: 2108

Alfa AF: 0.725 Hom.: 67819

Bravo AF: 0.764

Asia WGS AF: 0.865 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2206699; hg19: chr20-1985050;