dbSNP rs20417: PACERR:n.589C>G (chr1-186681189-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PACERR	NR_125801.1 link	n.536C>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PACERR	ENST00000608917.3 link	n.589C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 AFR exome

AC:

AN:

Gnomad4 AMR exome

AF:

0.00

AC:

AN:

Gnomad4 ASJ exome

AC:

AN:

Gnomad4 EAS exome

AC:

AN:

Gnomad4 SAS exome

AC:

AN:

Gnomad4 FIN exome

AC:

AN:

Gnomad4 NFE exome

AF:

0.167

AC:

AN:

Gnomad4 Remaining exome

AC:

AN:

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

AC:

0.3338

AN:

0.3338

Gnomad4 AMR

AF:

0.181

AC:

0.180734

AN:

0.180734

Gnomad4 ASJ

AF:

0.234

AC:

0.233987

AN:

0.233987

Gnomad4 EAS

AF:

0.0448

AC:

0.0448396

AN:

0.0448396

Gnomad4 SAS

AF:

0.165

AC:

0.164733

AN:

0.164733

Gnomad4 FIN

AF:

0.0866

AC:

0.0866491

AN:

0.0866491

Gnomad4 NFE

AF:

0.158

AC:

0.157899

AN:

0.157899

Gnomad4 OTH

AF:

0.210

AC:

0.210227

AN:

0.210227

Heterozygous variant carriers

1185

2370

3556

4741

5926

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Dec 10, 2022

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

Significance:other

Review Status:no assertion criteria provided

Collection Method:research

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

Mutation Taster

=99/1

polymorphism

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