rs6035126

chr20-1948896-C-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.442+1245C>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 0.14 in 152,064 control chromosomes in the GnomAD database, including 3,006 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 0.14 (3006 hom., cov: 32)
• Consequence: PDYN-AS1 NR_134520.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDYN-AS1	NR_134520.1	n.442+1245C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.406+1245C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21179 AN: 151946 Hom.: 2994 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.140 AC: 21233 AN: 152064 Hom.: 3006 Cov.: 32 AF XY: 0.136 AC XY: 10084 AN XY: 74358

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0208

Gnomad4 SAS AF: 0.0319

Gnomad4 FIN AF: 0.0394

Gnomad4 NFE AF: 0.0492

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0648 Hom.: 796

Bravo AF: 0.156

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.6
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6035126; hg19: chr20-1929542;