rs11709092

Variant names:

• chr3-48849594-A-C
• rs11709092
• ENST00000416209.2:n.1060A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 7 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416209.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKAR2A-AS1	NR_109996.1		n.1080A>C		non_coding_transcript_exon	Exon 2 of 2
	PRKAR2A-AS1	NR_109997.1		n.1001A>C		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKAR2A-AS1	ENST00000416209.2	TSL:2	n.1060A>C		non_coding_transcript_exon	Exon 2 of 2
	PRKAR2A-AS1	ENST00000655796.1		n.1087A>C		non_coding_transcript_exon	Exon 3 of 3
	PRKAR2A-AS1	ENST00000665061.1		n.1083A>C		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.111 AC: 8 AN: 72

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0603 AC: 9046 AN: 149950 Hom.: 385 Cov.: 32 AF XY: 0.0601 AC XY: 4392 AN XY: 73030

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: 2 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: 20 AN: 276

European-Non Finnish (NFE) AF: 0.0882 AC: 5971 AN: 67698

Other (OTH) AF: 0.0574 AC: 119 AN: 2072

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.87
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11709092; hg19: chr3-48887027;