rs7841060

Positions:

• chr8-127084232-T-G

Variant summary

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

The NR_109833.1(PRNCR1):​n.4359T>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 0.241 in 152,110 control chromosomes in the GnomAD database, including 4,738 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 0.24 (4738 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.4359T>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.4359T>G		non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1	n.418-5099A>C		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+77614T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36578 AN: 151992 Hom.: 4727 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.241 AC: 36619 AN: 152110 Hom.: 4738 Cov.: 32 AF XY: 0.239 AC XY: 17810 AN XY: 74374

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.214

Alfa AF: 0.213 Hom.: 1028

Bravo AF: 0.243

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7841060; hg19: chr8-128096477;