8-127086921-C-T

Variant names:

• chr8-127086921-C-T
• rs7007694
• ENST00000519282.1:n.590G>A

Variant summary

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

The ENST00000519282.1(ENSG00000224722):​n.590G>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 0.811 in 151,942 control chromosomes in the GnomAD database, including 50,257 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 0.81 (50257 hom., cov: 29)
  • Exomes 𝑓: 0.84 (513628 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000224722 ENST00000519282.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 20 publications found

Genes affected

ENSG00000224722 (HGNC:):

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

SRRM1P1 (HGNC:31861):

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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519282.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRNCR1	NR_109833.1		n.7048C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224722	ENST00000519282.1	TSL:6	n.590G>A		non_coding_transcript_exon	Exon 1 of 1
	PRNCR1	ENST00000635449.1	TSL:6	n.7048C>T		non_coding_transcript_exon	Exon 1 of 1
	CASC19	ENST00000642100.1		n.418-7788G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123169 AN: 151824 Hom.: 50244 Cov.: 29

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.805

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.837 AC: 1223136 AN: 1460952 Hom.: 513628 Cov.: 68 AF XY: 0.838 AC XY: 608961 AN XY: 726814

African (AFR) AF: 0.748 AC: 25032 AN: 33468

American (AMR) AF: 0.696 AC: 31052 AN: 44628

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 21457 AN: 26128

East Asian (EAS) AF: 0.681 AC: 27004 AN: 39654

South Asian (SAS) AF: 0.828 AC: 71396 AN: 86210

European-Finnish (FIN) AF: 0.854 AC: 45618 AN: 53404

Middle Eastern (MID) AF: 0.780 AC: 4494 AN: 5764

European-Non Finnish (NFE) AF: 0.852 AC: 947371 AN: 1111318

Other (OTH) AF: 0.823 AC: 49712 AN: 60378

GnomAD4 genome AF: 0.811 AC: 123225 AN: 151942 Hom.: 50257 Cov.: 29 AF XY: 0.809 AC XY: 60107 AN XY: 74256

African (AFR) AF: 0.748 AC: 30960 AN: 41402

American (AMR) AF: 0.782 AC: 11957 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2860 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3683 AN: 5104

South Asian (SAS) AF: 0.817 AC: 3933 AN: 4812

European-Finnish (FIN) AF: 0.857 AC: 9065 AN: 10572

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58029 AN: 67992

Other (OTH) AF: 0.800 AC: 1684 AN: 2106

Alfa AF: 0.813 Hom.: 35227

Bravo AF: 0.801

Asia WGS AF: 0.716 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.5
DANN	Benign	0.94
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7007694; hg19: chr8-128099166; COSMIC: COSV73056818;