Genetic Variant PCAT1:n.145+2014A>G (chr8-126591304-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000517773.5(PCAT1):n.145+2014A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,954 control chromosomes in the GnomAD database, including 16,567 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 0.46 ( 16567 hom., cov: 32)

Consequence

PCAT1
ENST00000517773.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.150

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375751	NR_188069.1 link	n.155+2014A>G	intron_variant	Intron 2 of 5
LOC105375751	NR_188070.1 link	n.155+2014A>G	intron_variant	Intron 2 of 3
LOC105375751	NR_188071.1 link	n.155+2014A>G	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PCAT1	ENST00000517773.5 link	n.145+2014A>G	intron_variant	Intron 2 of 2	3
PCAT1	ENST00000517915.2 link	n.119+2014A>G	intron_variant	Intron 2 of 2	3
PCAT1	ENST00000519880.5 link	n.156+2014A>G	intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70373

AN:

151834

Hom.:

16529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.579

Gnomad AMR

AF:

0.482

Gnomad ASJ

AF:

0.545

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.481

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.479

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

GnomAD4 genome

AF:

0.464

AC:

70449

AN:

151954

Hom.:

16567

Cov.:

AF XY:

0.466

AC XY:

34613

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.400

Gnomad4 AMR

AF:

0.482

Gnomad4 ASJ

AF:

0.545

Gnomad4 EAS

AF:

0.496

Gnomad4 SAS

AF:

0.482

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.481

Gnomad4 OTH

AF:

0.485

Alfa

AF:

0.488

Hom.:

37031

Bravo

AF:

0.461

Asia WGS

AF:

0.510

AC:

1771

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.3

DANN

Benign

0.60

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