rs2745559

Variant names:

• chr1-186682870-A-C
• rs2745559
• ENST00000608917.4:n.2763A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-186682870-A-C
• chr1-186682870-A-G
• chr1-186682870-A-T

Variant summary

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

The ENST00000608917.4(PACERR):​n.2763A>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 ENST00000608917.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608917.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PACERR	ENST00000608917.4	TSL:6	n.2763A>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.963 AC: 40029 AN: 41550

American (AMR) AF: 0.875 AC: 13368 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2615 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4993 AN: 5174

South Asian (SAS) AF: 0.790 AC: 3809 AN: 4820

European-Finnish (FIN) AF: 0.828 AC: 8753 AN: 10574

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56036 AN: 67982

Other (OTH) AF: 0.832 AC: 1752 AN: 2106

Alfa AF: 0.836 Hom.: 24449

Bravo AF: 0.879

Asia WGS AF: 0.881 AC: 3051 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.59
DANN	Benign	0.66
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2745559; hg19: chr1-186652002;