rs6045676

Positions:

• chr20-1960525-G-A
• chr20-1960525-G-C
• chr20-1960525-G-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.513-5079G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.041 (118 hom., cov: 19)
• Consequence: PDYN-AS1 NR_134520.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDYN-AS1	NR_134520.1	n.513-5079G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.477-5079G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0405 AC: 4727 AN: 116688 Hom.: 117 Cov.: 19

Gnomad AFR AF: 0.00978

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.0411

Gnomad EAS AF: 0.000420

Gnomad SAS AF: 0.00898

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.0389

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0290

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

GnomAD4 genome AF: 0.0405 AC: 4730 AN: 116730 Hom.: 118 Cov.: 19 AF XY: 0.0377 AC XY: 2059 AN XY: 54596

Gnomad4 AFR AF: 0.00976

Gnomad4 AMR AF: 0.0278

Gnomad4 ASJ AF: 0.0411

Gnomad4 EAS AF: 0.000421

Gnomad4 SAS AF: 0.00877

Gnomad4 FIN AF: 0.0386

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.0293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.45
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6045676; hg19: chr20-1941171;