Genetic Variant PDYN-AS1:n.477-5079G>C (chr20-1960525-G-C) – 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.477-5079G>C 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 0.40 ( 10802 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

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDYN-AS1	NR_134520.1 link	n.513-5079G>C		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.401

AC:

46461

AN:

115998

Hom.:

10777

Cov.:

show subpopulations

Gnomad AFR

AF:

0.639

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.288

Gnomad EAS

AF:

0.805

Gnomad SAS

AF:

0.574

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.390

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.382

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

GnomAD4 genome

AF:

0.401

AC:

46522

AN:

116046

Hom.:

10802

Cov.:

AF XY:

0.415

AC XY:

22548

AN XY:

54290

show subpopulations

African (AFR)

AF:

0.640

AC:

18986

AN:

29688

American (AMR)

AF:

0.366

AC:

3801

AN:

10394

Ashkenazi Jewish (ASJ)

AF:

0.288

AC:

888

AN:

3078

East Asian (EAS)

AF:

0.805

AC:

3818

AN:

4744

South Asian (SAS)

AF:

0.575

AC:

2291

AN:

3984

European-Finnish (FIN)

AF:

0.289

AC:

1219

AN:

4214

Middle Eastern (MID)

AF:

0.398

AC:

AN:

176

European-Non Finnish (NFE)

AF:

0.255

AC:

14633

AN:

57476

Other (OTH)

AF:

0.389

AC:

595

AN:

1528

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

1051

2102

3154

4205

5256

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.304

Hom.:

4005

Bravo

AF:

0.441

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.38

(source)

DANN

Benign

0.55

PhyloP100

-1.5

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