8-126591304-A-G

Variant names:

• chr8-126591304-A-G
• rs2385694
• ENST00000517773.6:n.545+2014A>G

Variant summary

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

The ENST00000517773.6(PCAT1):​n.545+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 ENST00000517773.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517773.6. 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+2014A>G		intron	N/A
	LOC105375751	NR_188070.1		n.155+2014A>G		intron	N/A
	LOC105375751	NR_188071.1		n.155+2014A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT1	ENST00000517773.6	TSL:3	n.545+2014A>G		intron	N/A
	PCAT1	ENST00000517915.3	TSL:3	n.208+2014A>G		intron	N/A
	PCAT1	ENST00000519880.5	TSL:4	n.156+2014A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70373 AN: 151834 Hom.: 16529 Cov.: 32

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.: 32 AF XY: 0.466 AC XY: 34613 AN XY: 74280

African (AFR) AF: 0.400 AC: 16554 AN: 41424

American (AMR) AF: 0.482 AC: 7359 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1891 AN: 3468

East Asian (EAS) AF: 0.496 AC: 2556 AN: 5150

South Asian (SAS) AF: 0.482 AC: 2322 AN: 4822

European-Finnish (FIN) AF: 0.510 AC: 5380 AN: 10558

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32698 AN: 67942

Other (OTH) AF: 0.485 AC: 1024 AN: 2110

Alfa AF: 0.479 Hom.: 75307

Bravo AF: 0.461

Asia WGS AF: 0.510 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2385694; hg19: chr8-127603549;