rs6993569

Positions:

• chr8-127071852-G-A

Variant summary

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

The ENST00000645463.1(PCAT1):​n.855+65234G>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 0.187 in 152,046 control chromosomes in the GnomAD database, including 4,839 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 0.19 (4839 hom., cov: 32)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

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.855+65234G>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000646670.1	n.1064+58078G>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000647190.2	n.1191+22552G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28382 AN: 151930 Hom.: 4823 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.187 AC: 28449 AN: 152046 Hom.: 4839 Cov.: 32 AF XY: 0.188 AC XY: 13994 AN XY: 74348

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0757

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0806 Hom.: 1877

Bravo AF: 0.205

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6993569; hg19: chr8-128084097;