8-127091810-G-T

Variant names:

• chr8-127091810-G-T
• rs7463708
• ENST00000635449.1:n.11937G>T

Variant summary

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

The NR_109833.1(PRNCR1):​n.11937G>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 0.271 in 149,672 control chromosomes in the GnomAD database, including 5,864 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 0.27 (5864 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.11937G>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.11937G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000642100.1	n.418-12677C>A		intron_variant	Intron 1 of 1
PCAT1	ENST00000645463.1	n.855+85192G>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.271 AC: 40506 AN: 149564 Hom.: 5854 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.271 AC: 40550 AN: 149668 Hom.: 5864 Cov.: 32 AF XY: 0.272 AC XY: 19888 AN XY: 73186

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.280

Alfa AF: 0.265 Hom.: 1386

Bravo AF: 0.273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7463708; hg19: chr8-128104055;