Genetic Variant PRNCR1:n.337C>T (chr8-127080210-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 ENST00000635449.1(PRNCR1):n.337C>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 0.504 in 151,740 control chromosomes in the GnomAD database, including 20,023 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 0.50 ( 20023 hom., cov: 31)

Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

PRNCR1
ENST00000635449.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.478

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1 link	n.337C>T		non_coding_transcript_exon_variant	Exon 1 of 1
PCAT2	NR_119373.1 link	n.102-1077G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PRNCR1	ENST00000635449.1 link	n.337C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000523510.1 link	n.102-1077G>A	intron_variant	Intron 1 of 3	3
CASC19	ENST00000641794.1 link	n.163-1077G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76342

AN:

151616

Hom.:

20008

Cov.:

show subpopulations

Gnomad AFR

AF:

0.629

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.623

Gnomad SAS

AF:

0.328

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.471

Gnomad OTH

AF:

0.491

GnomAD4 exome

AF:

0.333

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:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.504

AC:

76400

AN:

151734

Hom.:

20023

Cov.:

AF XY:

0.495

AC XY:

36670

AN XY:

74112

show subpopulations

African (AFR)

AF:

0.629

AC:

26003

AN:

41364

American (AMR)

AF:

0.359

AC:

5464

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

1330

AN:

3470

East Asian (EAS)

AF:

0.622

AC:

3193

AN:

5136

South Asian (SAS)

AF:

0.327

AC:

1570

AN:

4804

European-Finnish (FIN)

AF:

0.489

AC:

5146

AN:

10526

Middle Eastern (MID)

AF:

0.428

AC:

125

AN:

292

European-Non Finnish (NFE)

AF:

0.471

AC:

31976

AN:

67888

Other (OTH)

AF:

0.491

AC:

1035

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1865

3731

5596

7462

9327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

664

1328

1992

2656

3320

<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:

0.472

Hom.:

19179

Bravo

AF:

0.507

Asia WGS

AF:

0.462

AC:

1610

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.51

(source)

DANN

Benign

0.26

PhyloP100

-0.48

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over