rs16901946

Variant names:

• chr8-127088680-A-G
• rs16901946
• ENST00000635449.1:n.8807A>G

Variant summary

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

The ENST00000635449.1(PRNCR1):​n.8807A>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 0.0211 in 151,870 control chromosomes in the GnomAD database, including 220 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 0.021 (220 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRNCR1 ENST00000635449.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 19 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 (EAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.8807A>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.8807A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000642100.1	n.418-9547T>C		intron_variant	Intron 1 of 1
PCAT1	ENST00000645463.1	n.855+82062A>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3197 AN: 151752 Hom.: 217 Cov.: 31

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0128

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00728

Gnomad OTH AF: 0.0206

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 26

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0211 AC: 3208 AN: 151870 Hom.: 220 Cov.: 31 AF XY: 0.0244 AC XY: 1808 AN XY: 74212

African (AFR) AF: 0.0110 AC: 456 AN: 41396

American (AMR) AF: 0.0189 AC: 289 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1335 AN: 5152

South Asian (SAS) AF: 0.0902 AC: 433 AN: 4800

European-Finnish (FIN) AF: 0.0128 AC: 135 AN: 10514

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00728 AC: 495 AN: 67966

Other (OTH) AF: 0.0261 AC: 55 AN: 2108

Alfa AF: 0.0256 Hom.: 136

Bravo AF: 0.0221

Asia WGS AF: 0.193 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.65
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs16901946; hg19: chr8-128100925;