20-1973693-C-T

Variant names:

• chr20-1973693-C-T
• rs1022563
• ENST00000446562.1:n.1216+7350C>T

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+7350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,094 control chromosomes in the GnomAD database, including 4,621 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 0.21 (4621 hom., cov: 32)
• Consequence: PDYN-AS1 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 17 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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+7350C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.1216+7350C>T		intron	N/A
	PDYN-AS1	ENST00000651021.1		n.475+7350C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31258 AN: 151976 Hom.: 4618 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.206 AC: 31291 AN: 152094 Hom.: 4621 Cov.: 32 AF XY: 0.216 AC XY: 16071 AN XY: 74364

African (AFR) AF: 0.190 AC: 7889 AN: 41474

American (AMR) AF: 0.223 AC: 3399 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3470

East Asian (EAS) AF: 0.843 AC: 4357 AN: 5168

South Asian (SAS) AF: 0.461 AC: 2217 AN: 4810

European-Finnish (FIN) AF: 0.202 AC: 2139 AN: 10594

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10171 AN: 67990

Other (OTH) AF: 0.180 AC: 380 AN: 2108

Alfa AF: 0.182 Hom.: 894

Bravo AF: 0.204

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		1.5

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: rs1022563;

hg19: chr20-1954339;