rs2745559

Variant summary

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

The ENST00000608917.3(PACERR):​n.2270A>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 0.869 in 152,168 control chromosomes in the GnomAD database, including 57,823 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 0.87 ( 57823 hom., cov: 32)

Consequence

PACERR
ENST00000608917.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PACERRENST00000608917.3 linkn.2270A>C non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.869
AC:
132170
AN:
152050
Hom.:
57763
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.963
Gnomad AMI
AF:
0.804
Gnomad AMR
AF:
0.874
Gnomad ASJ
AF:
0.754
Gnomad EAS
AF:
0.965
Gnomad SAS
AF:
0.792
Gnomad FIN
AF:
0.828
Gnomad MID
AF:
0.690
Gnomad NFE
AF:
0.824
Gnomad OTH
AF:
0.830
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.869
AC:
132291
AN:
152168
Hom.:
57823
Cov.:
32
AF XY:
0.868
AC XY:
64541
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.963
Gnomad4 AMR
AF:
0.875
Gnomad4 ASJ
AF:
0.754
Gnomad4 EAS
AF:
0.965
Gnomad4 SAS
AF:
0.790
Gnomad4 FIN
AF:
0.828
Gnomad4 NFE
AF:
0.824
Gnomad4 OTH
AF:
0.832
Alfa
AF:
0.838
Hom.:
13815
Bravo
AF:
0.879
Asia WGS
AF:
0.881
AC:
3051
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.59
DANN
Benign
0.66

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: rs2745559; hg19: chr1-186652002; API