Genetic Variant PRKG1-AS1:n.583+1439C>T (chr10-52311959-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000420193.2(PRKG1-AS1):n.583+1439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 152,190 control chromosomes in the GnomAD database, including 1,928 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 0.097 ( 1928 hom., cov: 32)

Consequence

PRKG1-AS1
ENST00000420193.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119

Publications

2 publications found

Variant links:

Genes affected

PRKG1-AS1 (HGNC:45029): (PRKG1 antisense RNA 1)

PRKG1-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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKG1-AS1	NR_038277.1 link	n.583+1439C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PRKG1-AS1	ENST00000420193.2 link	n.583+1439C>T	intron_variant	Intron 2 of 8	3
PRKG1-AS1	ENST00000452247.8 link	n.959+1439C>T	intron_variant	Intron 2 of 6	5
PRKG1-AS1	ENST00000649494.1 link	n.962+1439C>T	intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes

AF:

0.0968

AC:

14723

AN:

152072

Hom.:

1920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0574

Gnomad ASJ

AF:

0.0732

Gnomad EAS

AF:

0.0141

Gnomad SAS

AF:

0.0544

Gnomad FIN

AF:

0.00302

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0931

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

GnomAD4 genome

AF:

0.0970

AC:

14766

AN:

152190

Hom.:

1928

Cov.:

AF XY:

0.0948

AC XY:

7056

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.297

AC:

12333

AN:

41492

American (AMR)

AF:

0.0574

AC:

877

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0732

AC:

254

AN:

3470

East Asian (EAS)

AF:

0.0139

AC:

AN:

5182

South Asian (SAS)

AF:

0.0536

AC:

258

AN:

4814

European-Finnish (FIN)

AF:

0.00302

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0105

AC:

715

AN:

68016

Other (OTH)

AF:

0.0945

AC:

200

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

568

1136

1704

2272

2840

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0881

Hom.:

278

Bravo

AF:

0.110

Asia WGS

AF:

0.0690

AC:

239

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.0

(source)

DANN

Benign

0.16

PhyloP100

0.12

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