rs72725879

chr8-127091724-C-T

Variant summary

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

The NR_109833.1(PRNCR1):n.11851C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,982 control chromosomes in the GnomAD database, including 5,905 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 0.26 (5905 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

Genes affected

PRNCR1 (HGNC:48942): (prostate cancer associated non-coding RNA 1)

CASC19 (HGNC:49476): (cancer susceptibility 19)

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRNCR1	NR_109833.1	n.11851C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRNCR1	ENST00000635449.1	n.11851C>T		non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1	n.418-12591G>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+85106C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39204 AN: 151864 Hom.: 5892 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.240

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.258 AC: 39270 AN: 151982 Hom.: 5905 Cov.: 32 AF XY: 0.261 AC XY: 19367 AN XY: 74288

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.246

Alfa AF: 0.222 Hom.: 506

Bravo AF: 0.271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.54
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72725879; hg19: chr8-128103969; COSMIC: COSV73056813;