Genetic Variant PRNCR1:n.1179C>T (chr8-127081052-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.1179C>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 0.203 in 152,162 control chromosomes in the GnomAD database, including 3,161 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 0.20 ( 3160 hom., cov: 32)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

PRNCR1
NR_109833.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.22

Publications

119 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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.1179C>T		non_coding_transcript_exon	Exon 1 of 1
	PCAT2	NR_119373.1		n.101+1069G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
PRNCR1	ENST00000635449.1	TSL:6	n.1179C>T	non_coding_transcript_exon	Exon 1 of 1
CASC19	ENST00000523510.1	TSL:3	n.101+1069G>A	intron	N/A
CASC19	ENST00000641794.1		n.162+1069G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30870

AN:

151932

Hom.:

3162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.328

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.181

GnomAD4 exome

AF:

0.134

AC:

AN:

112

Hom.:

Cov.:

AF XY:

0.185

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.158

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.100

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.203

AC:

30877

AN:

152050

Hom.:

3160

Cov.:

AF XY:

0.202

AC XY:

15014

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.212

AC:

8776

AN:

41436

American (AMR)

AF:

0.151

AC:

2306

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

648

AN:

3468

East Asian (EAS)

AF:

0.327

AC:

1691

AN:

5166

South Asian (SAS)

AF:

0.156

AC:

749

AN:

4814

European-Finnish (FIN)

AF:

0.209

AC:

2212

AN:

10606

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

13973

AN:

67964

Other (OTH)

AF:

0.179

AC:

379

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1264

2528

3793

5057

6321

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<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:

0.204

Hom.:

14399

Bravo

AF:

0.201

Asia WGS

AF:

0.187

AC:

653

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.019

(source)

DANN

Benign

0.41

PhyloP100

-3.2

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