dbSNP rs6444558: PYDC2-AS1:n.203+326C>A (chr3-191557710-C-A) – 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.203+326C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,928 control chromosomes in the GnomAD database, including 19,690 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 0.49 ( 19690 hom., cov: 32)

Consequence

PYDC2-AS1
ENST00000439804.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500

Publications

1 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYDC2-AS1	NR_120606.1 link	n.265+326C>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PYDC2-AS1	ENST00000439804.6 link	n.203+326C>A	intron_variant	Intron 2 of 4	2
PYDC2-AS1	ENST00000641055.1 link	n.338+326C>A	intron_variant	Intron 3 of 6
PYDC2-AS1	ENST00000641158.1 link	n.80-11890C>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73587

AN:

151810

Hom.:

19642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.725

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.437

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

GnomAD4 genome

AF:

0.485

AC:

73693

AN:

151928

Hom.:

19690

Cov.:

AF XY:

0.482

AC XY:

35750

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.726

AC:

30078

AN:

41446

American (AMR)

AF:

0.407

AC:

6203

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.401

AC:

1392

AN:

3472

East Asian (EAS)

AF:

0.302

AC:

1557

AN:

5162

South Asian (SAS)

AF:

0.496

AC:

2385

AN:

4808

European-Finnish (FIN)

AF:

0.381

AC:

4011

AN:

10526

Middle Eastern (MID)

AF:

0.425

AC:

124

AN:

292

European-Non Finnish (NFE)

AF:

0.394

AC:

26779

AN:

67952

Other (OTH)

AF:

0.441

AC:

930

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1750

3500

5250

7000

8750

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<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:

0.426

Hom.:

11980

Bravo

AF:

0.494

Asia WGS

AF:

0.487

AC:

1692

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.6

(source)

DANN

Benign

0.44

PhyloP100

-0.0050

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