Variant rs20417 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

other no assertion criteria provided O:1

Conservation

PhyloP100: -3.13

Variant links:

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]

PACERR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein	UniProt
PACERR	NR_125801.1 linkuse as main transcript	n.536C>G		non_coding_transcript_exon_variant	1/1

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30591

AN:

151892

Hom.:

3720

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.167

GnomAD4 genome

AF:

0.202

AC:

30652

AN:

152010

Hom.:

3740

Cov.:

AF XY:

0.197

AC XY:

14620

AN XY:

74322

show subpopulations

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.:

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

LINK: link

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over