rs13254738

Positions:

• chr8-127092098-C-A
• chr8-127092098-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 frequency of 0.562 in 155,062 control chromosomes in the GnomAD database, including 26,115 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 0.56 (25535 hom., cov: 31)
  • Exomes 𝑓: 0.60 (580 hom.)
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.12225C>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.12225C>A		non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1	n.418-12965G>T		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+85480C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85329 AN: 151810 Hom.: 25545 Cov.: 31

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.: 0 AF XY: 0.602 AC XY: 1001 AN XY: 1664

Gnomad4 AFR exome AF: 0.422

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.558

Gnomad4 EAS exome AF: 0.367

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.656

Gnomad4 NFE exome AF: 0.651

Gnomad4 OTH exome AF: 0.644

GnomAD4 genome AF: 0.562 AC: 85329 AN: 151928 Hom.: 25535 Cov.: 31 AF XY: 0.559 AC XY: 41513 AN XY: 74274

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.582

Alfa AF: 0.596 Hom.: 10149

Bravo AF: 0.539

Asia WGS AF: 0.449 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13254738; hg19: chr8-128104343;