20-1996399-A-T

Position:

• chr20-1996399-A-T

Variant summary

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

The NR_134520.1(PDYN-AS1):​n.1253-10533A>T 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 0.383 in 151,942 control chromosomes in the GnomAD database, including 13,119 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 0.38 (13119 hom., cov: 32)
• Consequence: PDYN-AS1 NR_134520.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDYN-AS1	NR_134520.1	n.1253-10533A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000651021.1	n.475+30056A>T		intron_variant, non_coding_transcript_variant
PDYN-AS1	ENST00000446562.1	n.1217-10533A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58144 AN: 151824 Hom.: 13095 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.383 AC: 58222 AN: 151942 Hom.: 13119 Cov.: 32 AF XY: 0.390 AC XY: 28941 AN XY: 74282

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.335

Alfa AF: 0.330 Hom.: 1203

Bravo AF: 0.389

Asia WGS AF: 0.719 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	9.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10854244; hg19: chr20-1977045;