20-1996399-A-T

Variant names:

• chr20-1996399-A-T
• rs10854244
• ENST00000446562.1:n.1217-10533A>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.1217-10533A>T variant causes a intron 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 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 3 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 = 0.819 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	NR_134520.1		n.1253-10533A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.1217-10533A>T		intron	N/A
	PDYN-AS1	ENST00000651021.1		n.475+30056A>T		intron	N/A

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

African (AFR) AF: 0.573 AC: 23745 AN: 41422

American (AMR) AF: 0.320 AC: 4891 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 782 AN: 3462

East Asian (EAS) AF: 0.840 AC: 4326 AN: 5152

South Asian (SAS) AF: 0.536 AC: 2583 AN: 4818

European-Finnish (FIN) AF: 0.326 AC: 3440 AN: 10566

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17373 AN: 67946

Other (OTH) AF: 0.335 AC: 706 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	9.4
DANN	Benign	0.58
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10854244; hg19: chr20-1977045;