Genetic Variant PDYN-AS1:n.477-5079G>C (chr20-1960525-G-C) – 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>C 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 0.401 (AC=46,522) in the gnomAD database across 116,046 control chromosomes, including 10,802 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.784. 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 0.40 ( 10802 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 = 0.7835 — 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>C		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>C		intron	N/A

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:

0.289

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:

0.289

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

Local populations

Turkish Variome

AF:

0.309

AC:

477

AN:

1542

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

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