ENST00000519319.2:n.263-36181G>A

Variant names:

• chr8-126970374-G-A
• rs1386468
• ENST00000519319.2:n.263-36181G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794
• Publications: 4 publications found

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]

LOC105375751 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	n.664-36181G>A		intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36255 AN: 151804 Hom.: 5237 Cov.: 31

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.: 31 AF XY: 0.246 AC XY: 18250 AN XY: 74240

African (AFR) AF: 0.0778 AC: 3227 AN: 41482

American (AMR) AF: 0.261 AC: 3978 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2147 AN: 5130

South Asian (SAS) AF: 0.286 AC: 1375 AN: 4800

European-Finnish (FIN) AF: 0.354 AC: 3724 AN: 10530

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19831 AN: 67954

Other (OTH) AF: 0.242 AC: 510 AN: 2106

Alfa AF: 0.245 Hom.: 697

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
PhyloP100		-0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1386468; hg19: chr8-127982619;