rs13252298

Variant names:

• chr8-127082911-A-G
• rs13252298
• ENST00000635449.1:n.3038A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635449.1(PRNCR1):​n.3038A>G 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 0.248 in 152,154 control chromosomes in the GnomAD database, including 5,804 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 0.25 (5804 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 ENST00000635449.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 78 publications found

Genes affected

PRNCR1 (HGNC:48942): (prostate cancer associated non-coding RNA 1)

CASC19 (HGNC:49476): (cancer susceptibility 19)

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.3038A>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.3038A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000642100.1	n.418-3778T>C		intron_variant	Intron 1 of 1
PCAT1	ENST00000645463.1	n.855+76293A>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37761 AN: 152036 Hom.: 5797 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.260

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.248 AC: 37776 AN: 152154 Hom.: 5804 Cov.: 32 AF XY: 0.259 AC XY: 19285 AN XY: 74394

African (AFR) AF: 0.0685 AC: 2844 AN: 41532

American (AMR) AF: 0.377 AC: 5759 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1783 AN: 5172

South Asian (SAS) AF: 0.473 AC: 2283 AN: 4824

European-Finnish (FIN) AF: 0.314 AC: 3322 AN: 10588

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19692 AN: 67992

Other (OTH) AF: 0.260 AC: 549 AN: 2110

Alfa AF: 0.280 Hom.: 22563

Bravo AF: 0.239

Asia WGS AF: 0.397 AC: 1379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.86
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs13252298; hg19: chr8-128095156; COSMIC: COSV73056794;