Genetic Variant PCAT1:n.263-36181G>A (chr8-126970374-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000519319.2(PCAT1):n.263-36181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,922 control chromosomes in the GnomAD database, including 5,242 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 0.24 ( 5242 hom., cov: 31)

Consequence

PCAT1
ENST00000519319.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.794

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:

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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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1 link	n.664-36181G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PCAT1	ENST00000519319.2 link	n.263-36181G>A	intron_variant	Intron 3 of 4	2
PCAT1	ENST00000643079.1 link	n.10-36181G>A	intron_variant	Intron 1 of 3
PCAT1	ENST00000643101.1 link	n.162-36181G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36255

AN:

151804

Hom.:

5237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0780

Gnomad AMI

AF:

0.424

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.418

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.245

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

GnomAD4 genome

AF:

0.239

AC:

36259

AN:

151922

Hom.:

5242

Cov.:

AF XY:

0.246

AC XY:

18250

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.0778

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.279

Gnomad4 EAS

AF:

0.419

Gnomad4 SAS

AF:

0.286

Gnomad4 FIN

AF:

0.354

Gnomad4 NFE

AF:

0.292

Gnomad4 OTH

AF:

0.242

Alfa

AF:

0.252

Hom.:

693

Bravo

AF:

0.225

Asia WGS

AF:

0.315

AC:

1094

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.1

DANN

Benign

0.46

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