rs12543663

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645463.1(PCAT1):​n.791+34624C>A variant causes a intron, non coding transcript 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 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000645463.1	n.791+34624C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.760

Alfa AF: 0.690 Hom.: 20052

Bravo AF: 0.760

Asia WGS AF: 0.827 AC: 2874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12543663; hg19: chr8-127924659;