Genetic Variant PDYN-AS1:n.1217-10130A>G (chr20-1996802-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000446562.1(PDYN-AS1):n.1217-10130A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 147,904 control chromosomes in the GnomAD database, including 2,374 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 0.14 ( 2374 hom., cov: 29)

Consequence

PDYN-AS1
ENST00000446562.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Publications

1 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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDYN-AS1	NR_134520.1 link	n.1253-10130A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDYN-AS1	ENST00000446562.1 link	n.1217-10130A>G		intron_variant	Intron 3 of 3	2
PDYN-AS1	ENST00000651021.1 link	n.475+30459A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20261

AN:

147796

Hom.:

2376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0773

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.0872

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.555

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.163

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.135

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

GnomAD4 genome

AF:

0.137

AC:

20255

AN:

147904

Hom.:

2374

Cov.:

AF XY:

0.146

AC XY:

10536

AN XY:

72104

show subpopulations

African (AFR)

AF:

0.0773

AC:

3033

AN:

39256

American (AMR)

AF:

0.0870

AC:

1302

AN:

14964

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

435

AN:

3452

East Asian (EAS)

AF:

0.554

AC:

2619

AN:

4728

South Asian (SAS)

AF:

0.366

AC:

1683

AN:

4596

European-Finnish (FIN)

AF:

0.219

AC:

2244

AN:

10262

Middle Eastern (MID)

AF:

0.159

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.126

AC:

8500

AN:

67398

Other (OTH)

AF:

0.141

AC:

290

AN:

2054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

748

1495

2243

2990

3738

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.306

Hom.:

10651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.23

(source)

DANN

Benign

0.89

PhyloP100

-1.7

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