rs2745559

chr1-186682870-A-Cchr1-186682870-A-Gchr1-186682870-A-T

Variant summary

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

The ENST00000608917.3(PACERR):n.2270A>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 0.869 in 152,168 control chromosomes in the GnomAD database, including 57,823 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 0.87 (57823 hom., cov: 32)
• Consequence: PACERR ENST00000608917.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

PACERR (HGNC:50552): (PTGS2 antisense NFKB1 complex-mediated expression regulator RNA) This gene represents transcription of a long non-coding RNA produced in antisense to the prostaglandin-endoperoxide synthase 2 (PTGS2) gene. This transcript interacts with NF-kB transcriptional regulators to promote expression of PTGS2. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PACERR	ENST00000608917.3	n.2270A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132170 AN: 152050 Hom.: 57763 Cov.: 32

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.869 AC: 132291 AN: 152168 Hom.: 57823 Cov.: 32 AF XY: 0.868 AC XY: 64541 AN XY: 74382

Gnomad4 AFR AF: 0.963

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.832

Alfa AF: 0.838 Hom.: 13815

Bravo AF: 0.879

Asia WGS AF: 0.881 AC: 3051 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.59
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2745559; hg19: chr1-186652002;