Genetic Variant PRKAR2A-AS1:n.1060A>C (chr3-48849594-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000416209.2(PRKAR2A-AS1):n.1060A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 150,036 control chromosomes in the GnomAD database, including 386 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 0.060 ( 385 hom., cov: 32)

Exomes 𝑓: 0.093 ( 1 hom. )

Consequence

PRKAR2A-AS1
ENST00000416209.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.289

Publications

7 publications found

Variant links:

Genes affected

PRKAR2A-AS1 (HGNC:40471): (PRKAR2A antisense RNA 1)

PRKAR2A-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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKAR2A-AS1	NR_109996.1 link	n.1080A>C		non_coding_transcript_exon_variant	Exon 2 of 2
PRKAR2A-AS1	NR_109997.1 link	n.1001A>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PRKAR2A-AS1	ENST00000416209.2 link	n.1060A>C	non_coding_transcript_exon_variant	Exon 2 of 2	2
PRKAR2A-AS1	ENST00000655796.1 link	n.1087A>C	non_coding_transcript_exon_variant	Exon 3 of 3
PRKAR2A-AS1	ENST00000665061.1 link	n.1083A>C	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0604

AC:

9049

AN:

149922

Hom.:

385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0169

Gnomad AMI

AF:

0.0868

Gnomad AMR

AF:

0.0528

Gnomad ASJ

AF:

0.0904

Gnomad EAS

AF:

0.000390

Gnomad SAS

AF:

0.0240

Gnomad FIN

AF:

0.0961

Gnomad MID

AF:

0.0695

Gnomad NFE

AF:

0.0882

Gnomad OTH

AF:

0.0583

GnomAD4 exome

AF:

0.0930

AC:

AN:

Hom.:

Cov.:

AF XY:

0.106

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.111

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0603

AC:

9046

AN:

149950

Hom.:

385

Cov.:

AF XY:

0.0601

AC XY:

4392

AN XY:

73030

show subpopulations

African (AFR)

AF:

0.0168

AC:

686

AN:

40758

American (AMR)

AF:

0.0528

AC:

796

AN:

15070

Ashkenazi Jewish (ASJ)

AF:

0.0904

AC:

313

AN:

3464

East Asian (EAS)

AF:

0.000392

AC:

AN:

5108

South Asian (SAS)

AF:

0.0238

AC:

113

AN:

4744

European-Finnish (FIN)

AF:

0.0961

AC:

947

AN:

9850

Middle Eastern (MID)

AF:

0.0725

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.0882

AC:

5971

AN:

67698

Other (OTH)

AF:

0.0574

AC:

119

AN:

2072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

413

826

1238

1651

2064

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.0686

Hom.:

Bravo

AF:

0.0556

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.3

(source)

DANN

Benign

0.87

PhyloP100

0.29

Mutation Taster

=100/0

polymorphism (auto)

(source)

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