Genetic Variant PRNCR1:n.1360C>T (chr8-127081233-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_109833.1(PRNCR1):n.1360C>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 0.557 in 151,676 control chromosomes in the GnomAD database, including 24,219 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 0.56 ( 24219 hom., cov: 33)

Exomes 𝑓: 0.38 ( 0 hom. )

Consequence

PRNCR1
NR_109833.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

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:

PCAT2 (HGNC:45089): (prostate cancer associated transcript 2)

PCAT2 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1 link	n.1360C>T		non_coding_transcript_exon_variant	Exon 1 of 1
PCAT2	NR_119373.1 link	n.101+888G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PRNCR1	ENST00000635449.1 link	n.1360C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000523510.1 link	n.101+888G>A	intron_variant	Intron 1 of 3	3
CASC19	ENST00000641794.1 link	n.162+888G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.557

AC:

84378

AN:

151548

Hom.:

24195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.650

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.634

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.539

Gnomad OTH

AF:

0.541

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.333

GnomAD4 genome

AF:

0.557

AC:

84445

AN:

151668

Hom.:

24219

Cov.:

AF XY:

0.546

AC XY:

40483

AN XY:

74120

show subpopulations

Gnomad4 AFR

AF:

0.671

Gnomad4 AMR

AF:

0.410

Gnomad4 ASJ

AF:

0.429

Gnomad4 EAS

AF:

0.633

Gnomad4 SAS

AF:

0.342

Gnomad4 FIN

AF:

0.534

Gnomad4 NFE

AF:

0.539

Gnomad4 OTH

AF:

0.541

Alfa

AF:

0.515

Hom.:

12121

Bravo

AF:

0.561

Asia WGS

AF:

0.480

AC:

1672

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

0.80

DANN

Benign

0.29

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