rs6045676

Variant names:

• chr20-1960525-G-A
• rs6045676
• ENST00000446562.1:n.477-5079G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-1960525-G-A
• chr20-1960525-G-C
• chr20-1960525-G-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.477-5079G>A variant causes a intron 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 ENST00000446562.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 13 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=-0.96).
• 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 rank	MANE	Protein	UniProt
PDYN-AS1	NR_134520.1	n.513-5079G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000446562.1	n.477-5079G>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.00976 AC: 294 AN: 30130

American (AMR) AF: 0.0278 AC: 291 AN: 10466

Ashkenazi Jewish (ASJ) AF: 0.0411 AC: 127 AN: 3092

East Asian (EAS) AF: 0.000421 AC: 2 AN: 4746

South Asian (SAS) AF: 0.00877 AC: 35 AN: 3992

European-Finnish (FIN) AF: 0.0386 AC: 163 AN: 4222

Middle Eastern (MID) AF: 0.0460 AC: 8 AN: 174

European-Non Finnish (NFE) AF: 0.0640 AC: 3687 AN: 57608

Other (OTH) AF: 0.0293 AC: 45 AN: 1534

Alfa AF: 0.00 Hom.: 4005

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
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs6045676; hg19: chr20-1941171;