rs12543663

Variant names:

• chr8-126912414-C-A
• rs12543663
• ENST00000519319.2:n.262+33934C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-126912414-C-A
• chr8-126912414-C-G
• chr8-126912414-C-T

Variant summary

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

The ENST00000519319.2(PCAT1):​n.262+33934C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,076 control chromosomes in the GnomAD database, including 43,795 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 0.75 (43795 hom., cov: 31)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 51 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519319.2. 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.663+34624C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT1	ENST00000519319.2	TSL:2	n.262+33934C>A		intron	N/A
	PCAT1	ENST00000643079.1		n.9+33934C>A		intron	N/A
	PCAT1	ENST00000643101.1		n.161+34624C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114645 AN: 151958 Hom.: 43745 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.755 AC: 114749 AN: 152076 Hom.: 43795 Cov.: 31 AF XY: 0.755 AC XY: 56140 AN XY: 74334

African (AFR) AF: 0.863 AC: 35825 AN: 41520

American (AMR) AF: 0.688 AC: 10508 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2445 AN: 3462

East Asian (EAS) AF: 0.937 AC: 4858 AN: 5182

South Asian (SAS) AF: 0.706 AC: 3395 AN: 4808

European-Finnish (FIN) AF: 0.706 AC: 7433 AN: 10530

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47678 AN: 67980

Other (OTH) AF: 0.760 AC: 1607 AN: 2114

Alfa AF: 0.717 Hom.: 42603

Bravo AF: 0.760

Asia WGS AF: 0.827 AC: 2874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.50
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs12543663; hg19: chr8-127924659;