dbSNP rs6035310: PDYN-AS1:n.476-20647A>C (chr20-2007953-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000651021.1(PDYN-AS1):n.476-20647A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,158 control chromosomes in the GnomAD database, including 3,556 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 0.19 ( 3556 hom., cov: 32)

Consequence

PDYN-AS1
ENST00000651021.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.185

Publications

2 publications found

Variant links:

Genes affected

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

PDYN-AS1 links:

Genome browser will be placed here

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000651021.1 link	n.476-20647A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29001

AN:

152040

Hom.:

3563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.661

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.164

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

GnomAD4 genome

AF:

0.191

AC:

28998

AN:

152158

Hom.:

3556

Cov.:

AF XY:

0.200

AC XY:

14889

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.150

AC:

6241

AN:

41522

American (AMR)

AF:

0.129

AC:

1971

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

466

AN:

3470

East Asian (EAS)

AF:

0.661

AC:

3420

AN:

5176

South Asian (SAS)

AF:

0.423

AC:

2042

AN:

4822

European-Finnish (FIN)

AF:

0.253

AC:

2676

AN:

10564

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11633

AN:

67978

Other (OTH)

AF:

0.168

AC:

356

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1145

2290

3434

4579

5724

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<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:

0.177

Hom.:

5624

Bravo

AF:

0.177

Asia WGS

AF:

0.521

AC:

1810

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.77

(source)

DANN

Benign

0.57

PhyloP100

0.18

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over