rs12334903

chr8-127038268-T-C

Variant summary

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

The ENST00000645463.1(PCAT1):n.855+31650T>C 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 0.438 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 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375751	XR_007061105.1	n.1799-25780T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.855+31650T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.450

Alfa AF: 0.407 Hom.: 8491

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12334903; hg19: chr8-128050513;