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

Variant summary

Our verdict is Benign. The variant received -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

Publications

5 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_109833.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRNCR1	NR_109833.1		n.1360C>T		non_coding_transcript_exon	Exon 1 of 1
	PCAT2	NR_119373.1		n.101+888G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
PRNCR1	ENST00000635449.1	TSL:6	n.1360C>T	non_coding_transcript_exon	Exon 1 of 1
CASC19	ENST00000523510.1	TSL:3	n.101+888G>A	intron	N/A
CASC19	ENST00000641794.1		n.162+888G>A	intron	N/A

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

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.692

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.557

AC:

84445

AN:

151668

Hom.:

24219

Cov.:

AF XY:

0.546

AC XY:

40483

AN XY:

74120

show subpopulations

African (AFR)

AF:

0.671

AC:

27735

AN:

41304

American (AMR)

AF:

0.410

AC:

6258

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1488

AN:

3466

East Asian (EAS)

AF:

0.633

AC:

3258

AN:

5148

South Asian (SAS)

AF:

0.342

AC:

1649

AN:

4822

European-Finnish (FIN)

AF:

0.534

AC:

5596

AN:

10482

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.539

AC:

36590

AN:

67872

Other (OTH)

AF:

0.541

AC:

1143

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1891

3782

5673

7564

9455

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.525

Hom.:

19395

Bravo

AF:

0.561

Asia WGS

AF:

0.480

AC:

1672

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.80

(source)

DANN

Benign

0.29

PhyloP100

-1.4

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over