dbSNP rs6045676: PDYN-AS1:n.477-5079G>A (chr20-1960525-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The NR_134520.1(PDYN-AS1):n.513-5079G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: NR_134520.1 is not a MANE Select or MANE Plus Clinical transcript for PDYN-AS1; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.0405 (AC=4,730) in the gnomAD database across 116,730 control chromosomes, including 118 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.0623. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

13 publications found

Variant links:

Genes affected

PDYN-AS1 (HGNC:53462): (PDYN antisense RNA 1)

PDYN-AS1 links:

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new If you want to explore the variant's impact on the transcript NR_134520.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Benign. The variant received -12 points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.0623 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NR_134520.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	NR_134520.1		n.513-5079G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDYN-AS1	ENST00000446562.1	TSL:2	n.477-5079G>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0405

AC:

4727

AN:

116688

Hom.:

117

Cov.:

show subpopulations

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.:

AF XY:

0.0377

AC XY:

2059

AN XY:

54596

show subpopulations

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:

AN:

4746

South Asian (SAS)

AF:

0.00877

AC:

AN:

3992

European-Finnish (FIN)

AF:

0.0386

AC:

163

AN:

4222

Middle Eastern (MID)

AF:

0.0460

AC:

AN:

174

European-Non Finnish (NFE)

AF:

0.0640

AC:

3687

AN:

57608

Other (OTH)

AF:

0.0293

AC:

AN:

1534

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

174

348

522

696

870

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

4005

Local populations

Turkish Variome

AF:

0.0389

AC:

AN:

1542

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.45

(source)

DANN

Benign

0.87

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over