8-127091692-T-C

Variant summary

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

The NR_109833.1(PRNCR1):n.11819T>C 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 0.588 in 152,004 control chromosomes in the GnomAD database, including 27,246 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 0.59 (27246 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRNCR1	NR_109833.1	n.11819T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRNCR1	ENST00000635449.1	n.11819T>C		non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1	n.418-12559A>G		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+85074T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89316 AN: 151886 Hom.: 27244 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.606

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: 0.588 AC: 89339 AN: 152004 Hom.: 27246 Cov.: 32 AF XY: 0.585 AC XY: 43472 AN XY: 74304

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.602

Alfa AF: 0.650 Hom.: 73904

Bravo AF: 0.570

Asia WGS AF: 0.461 AC: 1602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.1
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456315; hg19: chr8-128103937;