rs13254738

Variant names:

• chr8-127092098-C-A
• rs13254738
• ENST00000635449.1:n.12225C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 82 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_109833.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRNCR1	NR_109833.1		n.12225C>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRNCR1	ENST00000635449.1	TSL:6	n.12225C>A		non_coding_transcript_exon	Exon 1 of 1
	CASC19	ENST00000642100.1		n.418-12965G>T		intron	N/A
	PCAT1	ENST00000645463.1		n.855+85480C>A		intron	N/A

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

African (AFR) AF: 0.422 AC: 27 AN: 64

American (AMR) AF: 0.500 AC: 25 AN: 50

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 48 AN: 86

East Asian (EAS) AF: 0.367 AC: 171 AN: 466

South Asian (SAS) AF: 0.600 AC: 24 AN: 40

European-Finnish (FIN) AF: 0.656 AC: 252 AN: 384

Middle Eastern (MID) AF: 0.636 AC: 14 AN: 22

European-Non Finnish (NFE) AF: 0.651 AC: 1231 AN: 1890

Other (OTH) AF: 0.644 AC: 85 AN: 132

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

African (AFR) AF: 0.378 AC: 15647 AN: 41392

American (AMR) AF: 0.505 AC: 7719 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1590 AN: 5166

South Asian (SAS) AF: 0.638 AC: 3075 AN: 4820

European-Finnish (FIN) AF: 0.648 AC: 6827 AN: 10534

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46293 AN: 67956

Other (OTH) AF: 0.582 AC: 1228 AN: 2110

Alfa AF: 0.620 Hom.: 53440

Bravo AF: 0.539

Asia WGS AF: 0.449 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.50
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs13254738; hg19: chr8-128104343; COSMIC: COSV107545170;