20-1956829-A-G

Variant names:

• chr20-1956829-A-G
• rs2206698
• ENST00000446562.1:n.476+5281A>G

Variant summary

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

The ENST00000446562.1(PDYN-AS1):​n.476+5281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,080 control chromosomes in the GnomAD database, including 16,650 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 0.44 (16650 hom., cov: 32)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	NR_134520.1		n.512+5281A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.476+5281A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67106 AN: 151962 Hom.: 16605 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.442 AC: 67215 AN: 152080 Hom.: 16650 Cov.: 32 AF XY: 0.446 AC XY: 33149 AN XY: 74360

African (AFR) AF: 0.637 AC: 26427 AN: 41480

American (AMR) AF: 0.392 AC: 5994 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3472

East Asian (EAS) AF: 0.793 AC: 4098 AN: 5166

South Asian (SAS) AF: 0.564 AC: 2722 AN: 4822

European-Finnish (FIN) AF: 0.311 AC: 3292 AN: 10586

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21862 AN: 67970

Other (OTH) AF: 0.427 AC: 900 AN: 2110

Alfa AF: 0.366 Hom.: 23269

Bravo AF: 0.458

Asia WGS AF: 0.700 AC: 2431 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.4
DANN	Benign	0.80
PhyloP100		0.047

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2206698;

hg19: chr20-1937475;