rs689465

chr1-186681714-T-C

Variant summary

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

The ENST00000608917.3(PACERR):n.1114T>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 0.137 in 150,656 control chromosomes in the GnomAD database, including 1,487 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 0.14 (1487 hom., cov: 31)
• Consequence: PACERR ENST00000608917.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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.1114T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20550 AN: 150546 Hom.: 1478 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.137 AC: 20578 AN: 150656 Hom.: 1487 Cov.: 31 AF XY: 0.133 AC XY: 9811 AN XY: 73656

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0463

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.160

Alfa AF: 0.148 Hom.: 1606

Bravo AF: 0.143

Asia WGS AF: 0.131 AC: 457 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.95
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689465; hg19: chr1-186650846;