rs6045733

Variant names:

• chr20-1970212-G-A
• rs6045733
• ENST00000446562.1:n.1216+3869G>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.1216+3869G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,978 control chromosomes in the GnomAD database, including 23,143 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 0.52 (23143 hom., cov: 32)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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.1252+3869G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.1216+3869G>A		intron	N/A
	PDYN-AS1	ENST00000651021.1		n.475+3869G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78213 AN: 151860 Hom.: 23087 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.515 AC: 78331 AN: 151978 Hom.: 23143 Cov.: 32 AF XY: 0.518 AC XY: 38458 AN XY: 74274

African (AFR) AF: 0.801 AC: 33201 AN: 41462

American (AMR) AF: 0.474 AC: 7243 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.859 AC: 4437 AN: 5168

South Asian (SAS) AF: 0.550 AC: 2647 AN: 4812

European-Finnish (FIN) AF: 0.373 AC: 3927 AN: 10536

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24186 AN: 67952

Other (OTH) AF: 0.468 AC: 986 AN: 2108

Alfa AF: 0.414 Hom.: 10891

Bravo AF: 0.535

Asia WGS AF: 0.731 AC: 2541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.73
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6045733; hg19: chr20-1950858;