Genetic Variant PRNCR1:n.12225C>A (chr8-127092098-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019): 0P and 12B. BA1BP4_Strong

The NR_109833.1(PRNCR1):n.12225C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.562 (AC=87,206) in the gnomAD database across 155,062 control chromosomes, including 26,115 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.676. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 25535 hom., cov: 31)

Exomes 𝑓: 0.60 ( 580 hom. )

Consequence

PRNCR1
NR_109833.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.280

Publications

82 publications found

Variant links:

COSMIC-nc: COSV107545170

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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NR_109833.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Benign. The variant received -12 points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.6760 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

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

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRNCR1	NR_109833.1		n.12225C>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
PRNCR1	ENST00000635449.1	TSL:6	n.12225C>A	non_coding_transcript_exon	Exon 1 of 1
CASC19	ENST00000642100.1		n.418-12965G>T	intron	N/A
PCAT1	ENST00000645463.1		n.855+85480C>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.562

AC:

85329

AN:

151810

Hom.:

25545

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.784

Gnomad AMR

AF:

0.506

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.638

Gnomad FIN

AF:

0.648

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.681

Gnomad OTH

AF:

0.585

GnomAD4 exome

AF:

0.599

AC:

1877

AN:

3134

Hom.:

580

Cov.:

AF XY:

0.602

AC XY:

1001

AN XY:

1664

show subpopulations

African (AFR)

AF:

0.422

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.558

AC:

AN:

East Asian (EAS)

AF:

0.367

AC:

171

AN:

466

South Asian (SAS)

AF:

0.600

AC:

AN:

European-Finnish (FIN)

AF:

0.656

AC:

252

AN:

384

Middle Eastern (MID)

AF:

0.636

AC:

AN:

European-Non Finnish (NFE)

AF:

0.651

AC:

1231

AN:

1890

Other (OTH)

AF:

0.644

AC:

AN:

132

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

109

145

181

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.562

AC:

85329

AN:

151928

Hom.:

25535

Cov.:

AF XY:

0.559

AC XY:

41513

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.378

AC:

15647

AN:

41392

American (AMR)

AF:

0.505

AC:

7719

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.595

AC:

2063

AN:

3468

East Asian (EAS)

AF:

0.308

AC:

1590

AN:

5166

South Asian (SAS)

AF:

0.638

AC:

3075

AN:

4820

European-Finnish (FIN)

AF:

0.648

AC:

6827

AN:

10534

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.681

AC:

46293

AN:

67956

Other (OTH)

AF:

0.582

AC:

1228

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1775

3551

5326

7102

8877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.620

Hom.:

53440

Bravo

AF:

0.539

Asia WGS

AF:

0.449

AC:

1559

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.378

AC:

46317

AN:

122670

Turkish Variome

AF:

0.684

AC:

1058

AN:

1546

Hom.:

360

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.276

AC:

2472

AN:

8960

Hom.:

361

ABraOM SABE-WGS-1171

AF:

0.560

AC:

1311

AN:

2342

Hom.:

395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.86

(source)

DANN

Benign

0.50

PhyloP100

0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over