rs979200

Positions:

• chr8-126911475-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+33685C>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 0.447 in 152,070 control chromosomes in the GnomAD database, including 16,767 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 0.45 (16767 hom., cov: 32)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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.791+33685C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67890 AN: 151952 Hom.: 16751 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.447 AC: 67940 AN: 152070 Hom.: 16767 Cov.: 32 AF XY: 0.441 AC XY: 32768 AN XY: 74320

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.465

Alfa AF: 0.381 Hom.: 16660

Bravo AF: 0.472

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs979200; hg19: chr8-127923720;