8-127081052-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.1179C>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 0.203 in 152,162 control chromosomes in the GnomAD database, including 3,161 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 0.20 (3160 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

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]

PCAT2 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRNCR1	NR_109833.1	n.1179C>T		non_coding_transcript_exon_variant	1/1
PCAT2	NR_119373.1	n.101+1069G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRNCR1	ENST00000635449.1	n.1179C>T		non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1	n.418-1919G>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+74434C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30870 AN: 151932 Hom.: 3162 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.134 AC: 15 AN: 112 Hom.: 1 Cov.: 0 AF XY: 0.185 AC XY: 10 AN XY: 54

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.158

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.203 AC: 30877 AN: 152050 Hom.: 3160 Cov.: 32 AF XY: 0.202 AC XY: 15014 AN XY: 74334

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.179

Alfa AF: 0.205 Hom.: 7543

Bravo AF: 0.201

Asia WGS AF: 0.187 AC: 653 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	0.019
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1016343; hg19: chr8-128093297;