Genetic Variant PYDC2-AS1:n.80+64243C>T (chr3-191489847-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000439804.6(PYDC2-AS1):n.80+64243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,838 control chromosomes in the GnomAD database, including 18,699 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 0.48 ( 18699 hom., cov: 31)

Consequence

PYDC2-AS1
ENST00000439804.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.678

Publications

3 publications found

Variant links:

Genes affected

PYDC2-AS1 (HGNC:52874): (PYDC2 antisense RNA 1)

PYDC2-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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYDC2-AS1	NR_120606.1 link	n.82-56204C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PYDC2-AS1	ENST00000439804.6 link	n.80+64243C>T	intron_variant	Intron 1 of 4	2
PYDC2-AS1	ENST00000641055.1 link	n.215+16159C>T	intron_variant	Intron 2 of 6
PYDC2-AS1	ENST00000641158.1 link	n.79+64243C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.483

AC:

73257

AN:

151718

Hom.:

18674

Cov.:

show subpopulations

Gnomad AFR

AF:

0.648

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.681

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.427

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.443

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

GnomAD4 genome

AF:

0.483

AC:

73333

AN:

151838

Hom.:

18699

Cov.:

AF XY:

0.489

AC XY:

36280

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.648

AC:

26836

AN:

41394

American (AMR)

AF:

0.487

AC:

7431

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.302

AC:

1045

AN:

3462

East Asian (EAS)

AF:

0.681

AC:

3522

AN:

5174

South Asian (SAS)

AF:

0.470

AC:

2260

AN:

4808

European-Finnish (FIN)

AF:

0.427

AC:

4476

AN:

10484

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.389

AC:

26402

AN:

67934

Other (OTH)

AF:

0.443

AC:

935

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1838

3677

5515

7354

9192

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.402

Hom.:

21203

Bravo

AF:

0.495

Asia WGS

AF:

0.586

AC:

2031

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.24

(source)

DANN

Benign

0.39

PhyloP100

-0.68

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