Variant 8-127091724-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.969

Variant links:

Genes affected

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

PRNCR1 links:

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

CASC19 links:

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]

PCAT1 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
PRNCR1	NR_109833.1 linkuse as main transcript	n.11851C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
PRNCR1	ENST00000635449.1 linkuse as main transcript	n.11851C>T	non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1 linkuse as main transcript	n.418-12591G>A	intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1 linkuse as main transcript	n.855+85106C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39204

AN:

151864

Hom.:

5892

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

GnomAD4 genome

AF:

0.258

AC:

39270

AN:

151982

Hom.:

5905

Cov.:

AF XY:

0.261

AC XY:

19367

AN XY:

74288

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over