dbSNP rs2886242: PYDC2-AS1:n.80+46572A>G (chr3-191472176-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 ENST00000439804.6(PYDC2-AS1):n.80+46572A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,158 control chromosomes in the GnomAD database, including 1,426 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 0.12 ( 1426 hom., cov: 32)

Consequence

PYDC2-AS1
ENST00000439804.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.429

Publications

5 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYDC2-AS1	NR_120606.1 link	n.81+46572A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PYDC2-AS1	ENST00000439804.6 link	n.80+46572A>G	intron_variant	Intron 1 of 4	2
PYDC2-AS1	ENST00000641055.1 link	n.78-1375A>G	intron_variant	Intron 1 of 6
PYDC2-AS1	ENST00000641158.1 link	n.79+46572A>G	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18177

AN:

152040

Hom.:

1421

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0315

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.0668

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.137

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.126

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

GnomAD4 genome

AF:

0.120

AC:

18186

AN:

152158

Hom.:

1426

Cov.:

AF XY:

0.127

AC XY:

9416

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0316

AC:

1313

AN:

41554

American (AMR)

AF:

0.194

AC:

2958

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0668

AC:

232

AN:

3472

East Asian (EAS)

AF:

0.289

AC:

1495

AN:

5166

South Asian (SAS)

AF:

0.220

AC:

1061

AN:

4818

European-Finnish (FIN)

AF:

0.173

AC:

1827

AN:

10588

Middle Eastern (MID)

AF:

0.123

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.132

AC:

8966

AN:

67978

Other (OTH)

AF:

0.127

AC:

269

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

783

1565

2348

3130

3913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.126

Hom.:

4467

Bravo

AF:

0.114

Asia WGS

AF:

0.230

AC:

801

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.3

(source)

DANN

Benign

0.73

PhyloP100

0.43

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