Genetic Variant PRNCR1:n.11819T>C (chr8-127091692-T-C) – 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.11819T>C 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 0.588 in 152,004 control chromosomes in the GnomAD database, including 27,246 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 0.59 ( 27246 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

PRNCR1
NR_109833.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.507

Publications

84 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:

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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.

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 (SAS) allele frequency at 95% confidence interval = 0.669 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.11819T>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
PRNCR1	ENST00000635449.1	TSL:6	n.11819T>C	non_coding_transcript_exon	Exon 1 of 1
CASC19	ENST00000642100.1		n.418-12559A>G	intron	N/A
PCAT1	ENST00000645463.1		n.855+85074T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.588

AC:

89316

AN:

151886

Hom.:

27244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.460

Gnomad AMI

AF:

0.809

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.637

Gnomad EAS

AF:

0.296

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.651

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.675

Gnomad OTH

AF:

0.606

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

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)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.588

AC:

89339

AN:

152004

Hom.:

27246

Cov.:

AF XY:

0.585

AC XY:

43472

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.460

AC:

19060

AN:

41438

American (AMR)

AF:

0.548

AC:

8363

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.637

AC:

2211

AN:

3470

East Asian (EAS)

AF:

0.296

AC:

1532

AN:

5172

South Asian (SAS)

AF:

0.675

AC:

3252

AN:

4820

European-Finnish (FIN)

AF:

0.651

AC:

6876

AN:

10558

Middle Eastern (MID)

AF:

0.605

AC:

178

AN:

294

European-Non Finnish (NFE)

AF:

0.675

AC:

45857

AN:

67970

Other (OTH)

AF:

0.602

AC:

1274

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1780

3560

5341

7121

8901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

746

1492

2238

2984

3730

<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:

0.644

Hom.:

144661

Bravo

AF:

0.570

Asia WGS

AF:

0.461

AC:

1602

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

3.1

(source)

DANN

Benign

0.81

PhyloP100

0.51

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

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over