rs12334903

Variant names:

• chr8-127038268-T-C
• rs12334903
• ENST00000643594.2:n.216-25780T>C

Variant summary

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

The ENST00000643594.2(PCAT1):​n.216-25780T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,674 control chromosomes in the GnomAD database, including 15,434 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 0.44 (15434 hom., cov: 32)
• Consequence: PCAT1 ENST00000643594.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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	ENST00000643594.2	n.216-25780T>C		intron_variant	Intron 2 of 2
PCAT1	ENST00000644627.1	n.712-25780T>C		intron_variant	Intron 4 of 4
PCAT1	ENST00000644733.1	n.126-25780T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66380 AN: 151556 Hom.: 15397 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.438 AC: 66475 AN: 151674 Hom.: 15434 Cov.: 32 AF XY: 0.431 AC XY: 31943 AN XY: 74124

African (AFR) AF: 0.585 AC: 24206 AN: 41382

American (AMR) AF: 0.435 AC: 6615 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1067 AN: 5114

South Asian (SAS) AF: 0.380 AC: 1832 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3097 AN: 10554

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 26986 AN: 67808

Other (OTH) AF: 0.450 AC: 950 AN: 2112

Alfa AF: 0.404 Hom.: 15121

Bravo AF: 0.453

Asia WGS AF: 0.353 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.69
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs12334903; hg19: chr8-128050513;