Variant chr3-48849594-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

Variant links:

Genes affected

PRKAR2A-AS1 (HGNC:):

PRKAR2A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PRKAR2A-AS1	NR_109996.1 linkuse as main transcript	n.1080A>C		non_coding_transcript_exon_variant	2/2
PRKAR2A-AS1	NR_109997.1 linkuse as main transcript	n.1001A>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
PRKAR2A-AS1	ENST00000416209.2 linkuse as main transcript	n.1060A>C	non_coding_transcript_exon_variant	2/2	2
PRKAR2A-AS1	ENST00000655796.1 linkuse as main transcript	n.1087A>C	non_coding_transcript_exon_variant	3/3
PRKAR2A-AS1	ENST00000665061.1 linkuse as main transcript	n.1083A>C	non_coding_transcript_exon_variant	2/2
PRKAR2A-AS1	ENST00000669166.1 linkuse as main transcript	n.1562A>C	non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.111

GnomAD4 genome

AF:

0.0603

AC:

9046

AN:

149950

Hom.:

385

Cov.:

AF XY:

0.0601

AC XY:

4392

AN XY:

73030

show subpopulations

Gnomad4 AFR

AF:

0.0168

Gnomad4 AMR

AF:

0.0528

Gnomad4 ASJ

AF:

0.0904

Gnomad4 EAS

AF:

0.000392

Gnomad4 SAS

AF:

0.0238

Gnomad4 FIN

AF:

0.0961

Gnomad4 NFE

AF:

0.0882

Gnomad4 OTH

AF:

0.0574

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

DANN

Benign

0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over