rs7841060

Variant names:

• chr8-127084232-T-G
• rs7841060
• ENST00000635449.1:n.4359T>G

Variant summary

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

The ENST00000635449.1(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 ENST00000635449.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 28 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=-0.89).
• 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 rank	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.4359T>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.4359T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
CASC19	ENST00000642100.1	n.418-5099A>C		intron_variant	Intron 1 of 1
PCAT1	ENST00000645463.1	n.855+77614T>G		intron_variant	Intron 6 of 6

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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.336 AC: 13945 AN: 41444

American (AMR) AF: 0.169 AC: 2583 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3470

East Asian (EAS) AF: 0.330 AC: 1709 AN: 5178

South Asian (SAS) AF: 0.158 AC: 765 AN: 4828

European-Finnish (FIN) AF: 0.208 AC: 2206 AN: 10588

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14138 AN: 67992

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.222 Hom.: 1923

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7841060; hg19: chr8-128096477;