chr8-127081233-C-T

Variant names:

• chr8-127081233-C-T
• rs1551510
• ENST00000635449.1:n.1360C>T

Variant summary

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

The ENST00000635449.1(PRNCR1):​n.1360C>T 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 0.557 in 151,676 control chromosomes in the GnomAD database, including 24,219 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 (24219 hom., cov: 33)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: PRNCR1 ENST00000635449.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 5 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]

PCAT2 (HGNC:45089): (prostate cancer associated transcript 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.1360C>T		non_coding_transcript_exon_variant	Exon 1 of 1
PCAT2	NR_119373.1	n.101+888G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRNCR1	ENST00000635449.1	n.1360C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000523510.1	n.101+888G>A		intron_variant	Intron 1 of 3	3
CASC19	ENST00000641794.1	n.162+888G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84378 AN: 151548 Hom.: 24195 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

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) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.557 AC: 84445 AN: 151668 Hom.: 24219 Cov.: 33 AF XY: 0.546 AC XY: 40483 AN XY: 74120

African (AFR) AF: 0.671 AC: 27735 AN: 41304

American (AMR) AF: 0.410 AC: 6258 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3466

East Asian (EAS) AF: 0.633 AC: 3258 AN: 5148

South Asian (SAS) AF: 0.342 AC: 1649 AN: 4822

European-Finnish (FIN) AF: 0.534 AC: 5596 AN: 10482

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36590 AN: 67872

Other (OTH) AF: 0.541 AC: 1143 AN: 2112

Alfa AF: 0.525 Hom.: 19395

Bravo AF: 0.561

Asia WGS AF: 0.480 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.29
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1551510; hg19: chr8-128093478;