rs11709092

chr3-48849594-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109996.1(PRKAR2A-AS1):n.1080A>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 NR_109996.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

Genes affected

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

ACMG classification

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	UniProt
PRKAR2A-AS1	NR_109996.1	n.1080A>C		non_coding_transcript_exon_variant	2/2
PRKAR2A-AS1	NR_109997.1	n.1001A>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKAR2A-AS1	ENST00000655796.1	n.1087A>C		non_coding_transcript_exon_variant	3/3
PRKAR2A-AS1	ENST00000416209.2	n.1060A>C		non_coding_transcript_exon_variant	2/2	2
PRKAR2A-AS1	ENST00000665061.1	n.1083A>C		non_coding_transcript_exon_variant	2/2
PRKAR2A-AS1	ENST00000669166.1	n.1562A>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9049 AN: 149922 Hom.: 385 Cov.: 32

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: 8 AN: 86 Hom.: 1 Cov.: 0 AF XY: 0.106 AC XY: 7 AN XY: 66

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.: 32 AF XY: 0.0601 AC XY: 4392 AN XY: 73030

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.: 56

Bravo AF: 0.0556

Asia WGS AF: 0.0110 AC: 39 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

Other links and lift over

dbSNP: rs11709092; hg19: chr3-48887027;