rs20417

chr1-186681189-C-Gchr1-186681189-C-T

Variant summary

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

The NR_125801.1(PACERR):n.536C>G 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 0.202 in 152,018 control chromosomes in the GnomAD database, including 3,740 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars).

• Frequency:
  • Genomes: 𝑓 0.20 (3740 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: PACERR NR_125801.1 non_coding_transcript_exon
• Clinical Significance: other no assertion criteria provided O:1
• Conservation: PhyloP100: -3.13

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PACERR	NR_125801.1	n.536C>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PACERR	ENST00000608917.3	n.589C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30591 AN: 151892 Hom.: 3720 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 AMR exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.202 AC: 30652 AN: 152010 Hom.: 3740 Cov.: 32 AF XY: 0.197 AC XY: 14620 AN XY: 74322

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0448

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0866

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.210

Alfa AF: 0.0650 Hom.: 82

Bravo AF: 0.214

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Significance: other

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Cholangiocarcinoma Other:1

other, no assertion criteria provided

research

Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin

Dec 10, 2022

No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.84
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs20417; hg19: chr1-186650321;