rs6993569

Variant names:

• chr8-127071852-G-A
• rs6993569
• ENST00000645463.1:n.855+65234G>A

Variant summary

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

The ENST00000645463.1(PCAT1):​n.855+65234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,046 control chromosomes in the GnomAD database, including 4,839 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 0.19 (4839 hom., cov: 32)
• Consequence: PCAT1 ENST00000645463.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000645463.1	n.855+65234G>A		intron_variant	Intron 6 of 6
PCAT1	ENST00000646670.1	n.1064+58078G>A		intron_variant	Intron 5 of 6
PCAT1	ENST00000647190.2	n.1191+22552G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28382 AN: 151930 Hom.: 4823 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.187 AC: 28449 AN: 152046 Hom.: 4839 Cov.: 32 AF XY: 0.188 AC XY: 13994 AN XY: 74348

African (AFR) AF: 0.447 AC: 18511 AN: 41438

American (AMR) AF: 0.162 AC: 2476 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1469 AN: 5176

South Asian (SAS) AF: 0.124 AC: 597 AN: 4818

European-Finnish (FIN) AF: 0.0757 AC: 801 AN: 10588

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0587 AC: 3990 AN: 67974

Other (OTH) AF: 0.166 AC: 351 AN: 2112

Alfa AF: 0.0976 Hom.: 6678

Bravo AF: 0.205

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.38
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6993569; hg19: chr8-128084097;