rs6981122

Positions:

• chr8-127082215-A-C
• chr8-127082215-A-T

Variant summary

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

The NR_109833.1(PRNCR1):​n.2342A>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 0.581 in 151,950 control chromosomes in the GnomAD database, including 26,369 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 0.58 (26369 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 NR_109833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

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

PCAT2 (HGNC:):

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.2342A>C		non_coding_transcript_exon_variant	1/1
PCAT2	NR_119373.1	n.7T>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.2342A>C		non_coding_transcript_exon_variant	1/1
CASC19	ENST00000642100.1	n.418-3082T>G		intron_variant, non_coding_transcript_variant
PCAT1	ENST00000645463.1	n.855+75597A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88249 AN: 151832 Hom.: 26345 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.567

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: 0.581 AC: 88318 AN: 151950 Hom.: 26369 Cov.: 32 AF XY: 0.570 AC XY: 42305 AN XY: 74262

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.568

Alfa AF: 0.558 Hom.: 23326

Bravo AF: 0.583

Asia WGS AF: 0.502 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6981122; hg19: chr8-128094460;