20-1959858-T-C

Variant names:

• chr20-1959858-T-C
• rs6045666
• ENST00000446562.1:n.477-5746T>C

Variant summary

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

The ENST00000446562.1(PDYN-AS1):​n.477-5746T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 150,306 control chromosomes in the GnomAD database, including 15,612 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 0.42 (15612 hom., cov: 28)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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.513-5746T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.477-5746T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 63434 AN: 150202 Hom.: 15574 Cov.: 28

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.423 AC: 63531 AN: 150306 Hom.: 15612 Cov.: 28 AF XY: 0.426 AC XY: 31294 AN XY: 73380

African (AFR) AF: 0.648 AC: 26371 AN: 40686

American (AMR) AF: 0.355 AC: 5357 AN: 15102

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3466

East Asian (EAS) AF: 0.794 AC: 4056 AN: 5108

South Asian (SAS) AF: 0.548 AC: 2609 AN: 4758

European-Finnish (FIN) AF: 0.295 AC: 2992 AN: 10152

Middle Eastern (MID) AF: 0.407 AC: 118 AN: 290

European-Non Finnish (NFE) AF: 0.292 AC: 19810 AN: 67754

Other (OTH) AF: 0.394 AC: 824 AN: 2092

Alfa AF: 0.347 Hom.: 2543

Bravo AF: 0.438

Asia WGS AF: 0.691 AC: 2400 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		-0.63

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: rs6045666;

hg19: chr20-1940504;