8-127086921-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.7048C>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 0.811 in 151,942 control chromosomes in the GnomAD database, including 50,257 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 0.81 (50257 hom., cov: 29)
  • Exomes 𝑓: 0.84 (513628 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

(HGNC:):

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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRNCR1	NR_109833.1	n.7048C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000519282.1	n.590G>A		non_coding_transcript_exon_variant	1/1
PRNCR1	ENST00000635449.1	n.7048C>T		non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1	n.418-7788G>A		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+80303C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123169 AN: 151824 Hom.: 50244 Cov.: 29

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.805

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.837 AC: 1223136 AN: 1460952 Hom.: 513628 Cov.: 68 AF XY: 0.838 AC XY: 608961 AN XY: 726814

Gnomad4 AFR exome AF: 0.748

Gnomad4 AMR exome AF: 0.696

Gnomad4 ASJ exome AF: 0.821

Gnomad4 EAS exome AF: 0.681

Gnomad4 SAS exome AF: 0.828

Gnomad4 FIN exome AF: 0.854

Gnomad4 NFE exome AF: 0.852

Gnomad4 OTH exome AF: 0.823

GnomAD4 genome AF: 0.811 AC: 123225 AN: 151942 Hom.: 50257 Cov.: 29 AF XY: 0.809 AC XY: 60107 AN XY: 74256

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.800

Alfa AF: 0.825 Hom.: 14056

Bravo AF: 0.801

Asia WGS AF: 0.716 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	6.5
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7007694; hg19: chr8-128099166; COSMIC: COSV73056818;