Variant 8-127071852-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000645463.1(PCAT1):n.855+65234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,046 control chromosomes in the GnomAD database, including 4,839 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 0.19 ( 4839 hom., cov: 32)

Consequence

PCAT1
ENST00000645463.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.583

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:

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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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
PCAT1	ENST00000645463.1 link	n.855+65234G>A	intron_variant
PCAT1	ENST00000646670.1 link	n.1064+58078G>A	intron_variant
PCAT1	ENST00000647190.2 link	n.1191+22552G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28382

AN:

151930

Hom.:

4823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.446

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.0481

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.0757

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0587

Gnomad OTH

AF:

0.162

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

GnomAD4 genome

AF:

0.187

AC:

28449

AN:

152046

Hom.:

4839

Cov.:

AF XY:

0.188

AC XY:

13994

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.447

Gnomad4 AMR

AF:

0.162

Gnomad4 ASJ

AF:

0.0481

Gnomad4 EAS

AF:

0.284

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.0757

Gnomad4 NFE

AF:

0.0587

Gnomad4 OTH

AF:

0.166

Alfa

AF:

0.0806

Hom.:

1877

Bravo

AF:

0.205

Asia WGS

AF:

0.232

AC:

805

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.51

DANN

Benign

0.38

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