Variant chr8-126647291-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000520512.1(PCAT1):n.137-19254A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,676 control chromosomes in the GnomAD database, including 17,105 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 0.47 ( 17105 hom., cov: 30)

Consequence

PCAT1
ENST00000520512.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.312

Variant links:

Genes affected

PCAT1 (HGNC:43022): (prostate cancer associated transcript 1) This gene produces a long non-coding RNA that promotes cell proliferation and is upregulated in prostate, colorectal, and other cancers. This RNA negatively regulates the BRCA2 tumor suppressor protein and positively regulates Myc oncoprotein. It contains binding sites for microRNAs, and may act as a sponge for microRNAs that regulate cell growth pathways. [provided by RefSeq, Dec 2017]

PCAT1 links:

LOC105375751 (HGNC:):

LOC105375751 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105375751	NR_188069.1 link	n.155+58001A>G	intron_variant
LOC105375751	NR_188070.1 link	n.155+58001A>G	intron_variant
LOC105375751	NR_188071.1 link	n.155+58001A>G	intron_variant
LOC105375751	NR_188072.1 link	n.155+58001A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
PCAT1	ENST00000519880.5 link	n.156+58001A>G	intron_variant	4
PCAT1	ENST00000520512.1 link	n.137-19254A>G	intron_variant	3
PCAT1	ENST00000645463.1 link	n.283+54873A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71046

AN:

151556

Hom.:

17102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.382

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.691

Gnomad SAS

AF:

0.526

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.479

Gnomad OTH

AF:

0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.468

AC:

71056

AN:

151676

Hom.:

17105

Cov.:

AF XY:

0.479

AC XY:

35484

AN XY:

74096

show subpopulations

Gnomad4 AFR

AF:

0.381

Gnomad4 AMR

AF:

0.457

Gnomad4 ASJ

AF:

0.467

Gnomad4 EAS

AF:

0.691

Gnomad4 SAS

AF:

0.526

Gnomad4 FIN

AF:

0.643

Gnomad4 NFE

AF:

0.479

Gnomad4 OTH

AF:

0.443

Alfa

AF:

0.467

Hom.:

24145

Bravo

AF:

0.451

Asia WGS

AF:

0.570

AC:

1983

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.0

DANN

Benign

0.32

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over