chr8-126978010-C-T

Position:

• chr8-126978010-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000645463.1(PCAT1):​n.792-28545C>T 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 0.0286 in 152,282 control chromosomes in the GnomAD database, including 67 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 0.029 (67 hom., cov: 33)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

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=-0.7).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0286 (4358/152282) while in subpopulation AFR AF= 0.043 (1787/41550). AF 95% confidence interval is 0.0413. There are 67 homozygotes in gnomad4. There are 2148 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 67 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.792-28545C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0286 AC: 4351 AN: 152164 Hom.: 67 Cov.: 33

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0286 AC: 4358 AN: 152282 Hom.: 67 Cov.: 33 AF XY: 0.0288 AC XY: 2148 AN XY: 74460

Gnomad4 AFR AF: 0.0430

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0340

Gnomad4 NFE AF: 0.0248

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0258 Hom.: 31

Bravo AF: 0.0280

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs753228; hg19: chr8-127990255;