8-126807309-C-T

Variant names:

• chr8-126807309-C-T
• rs6987948
• ENST00000520224.2:n.440-12982G>A

Variant summary

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

The ENST00000520224.2(ENSG00000253573):​n.440-12982G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,822 control chromosomes in the GnomAD database, including 23,755 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 0.54 (23755 hom., cov: 32)
• Consequence: ENSG00000253573 ENST00000520224.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 1 publications found

Genes affected

ENSG00000253573 (HGNC:):

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520224.2. 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
	LOC105375751	NR_188069.1		n.545-70363C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253573	ENST00000520224.2	TSL:3	n.440-12982G>A		intron	N/A
	PCAT1	ENST00000645198.1		n.22-70363C>T		intron	N/A
	PCAT1	ENST00000645463.1		n.673-70363C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81903 AN: 151704 Hom.: 23702 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.544

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.540 AC: 82012 AN: 151822 Hom.: 23755 Cov.: 32 AF XY: 0.546 AC XY: 40490 AN XY: 74144

African (AFR) AF: 0.766 AC: 31736 AN: 41442

American (AMR) AF: 0.562 AC: 8582 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3105 AN: 5174

South Asian (SAS) AF: 0.556 AC: 2675 AN: 4812

European-Finnish (FIN) AF: 0.470 AC: 4925 AN: 10470

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

European-Non Finnish (NFE) AF: 0.407 AC: 27613 AN: 67870

Other (OTH) AF: 0.549 AC: 1162 AN: 2116

Alfa AF: 0.292 Hom.: 610

Bravo AF: 0.558

Asia WGS AF: 0.601 AC: 2088 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.12
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs6987948; hg19: chr8-127819554;