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 ACMG points: 0P and 12B. BP4_StrongBA1

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

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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000446562.1, 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.

ACMG classification

Classification was made for transcript

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.

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

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

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over