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rs20417

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: đť‘“ 0.20 ( 3740 hom., cov: 32)
Exomes đť‘“: 0.13 ( 0 hom. )

Consequence

PACERR
NR_125801.1 non_coding_transcript_exon

Scores

2

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]

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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 UniProt
PACERRNR_125801.1 linkuse as main transcriptn.536C>G non_coding_transcript_exon_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PACERRENST00000608917.3 linkuse as main transcriptn.589C>G non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.201
AC:
30591
AN:
151892
Hom.:
3720
Cov.:
32
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:
1
AN:
8
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
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.:
32
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.:
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
LINK: link

Submissions by phenotype

Cholangiocarcinoma Other:1
other, no assertion criteria providedresearchDepartment of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin BerlinDec 10, 2022No 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.

Other links and lift over

dbSNP: rs20417; hg19: chr1-186650321; API