20-1956829-A-G

Position:

• chr20-1956829-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134520.1(PDYN-AS1):​n.512+5281A>G variant causes a intron, non coding transcript 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 NR_134520.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

PDYN-AS1 (HGNC:53462): (PDYN antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDYN-AS1	NR_134520.1	n.512+5281A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.476+5281A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.427

Alfa AF: 0.343 Hom.: 13584

Bravo AF: 0.458

Asia WGS AF: 0.700 AC: 2431 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206698; hg19: chr20-1937475;