ENST00000519880.5:n.156+58001A>G

Variant names:

• chr8-126647291-A-G
• rs2385686
• ENST00000519880.5:n.156+58001A>G

Variant summary

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

The ENST00000519880.5(PCAT1):​n.156+58001A>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 ENST00000519880.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519880.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375751	NR_188069.1		n.155+58001A>G		intron	N/A
	LOC105375751	NR_188070.1		n.155+58001A>G		intron	N/A
	LOC105375751	NR_188071.1		n.155+58001A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT1	ENST00000519880.5	TSL:4	n.156+58001A>G		intron	N/A
	PCAT1	ENST00000520512.1	TSL:3	n.137-19254A>G		intron	N/A
	PCAT1	ENST00000645463.1		n.283+54873A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71046 AN: 151556 Hom.: 17102 Cov.: 30

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.: 30 AF XY: 0.479 AC XY: 35484 AN XY: 74096

African (AFR) AF: 0.381 AC: 15725 AN: 41310

American (AMR) AF: 0.457 AC: 6964 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3545 AN: 5128

South Asian (SAS) AF: 0.526 AC: 2527 AN: 4804

European-Finnish (FIN) AF: 0.643 AC: 6757 AN: 10512

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32496 AN: 67904

Other (OTH) AF: 0.443 AC: 934 AN: 2110

Alfa AF: 0.465 Hom.: 33075

Bravo AF: 0.451

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.32
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2385686; hg19: chr8-127659536;