chr8-126999692-T-C

Variant names:

• chr8-126999692-T-C
• rs10086908
• ENST00000519319.2:n.263-6863T>C

Variant summary

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

The ENST00000519319.2(PCAT1):​n.263-6863T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,998 control chromosomes in the GnomAD database, including 6,006 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 0.28 (6006 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 78 publications found

Genes affected

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]

LOC105375751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519319.2. 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.664-6863T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT1	ENST00000519319.2	TSL:2	n.263-6863T>C		intron	N/A
	PCAT1	ENST00000643079.1		n.10-6863T>C		intron	N/A
	PCAT1	ENST00000643101.1		n.162-6863T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41968 AN: 151880 Hom.: 5990 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.276 AC: 42012 AN: 151998 Hom.: 6006 Cov.: 32 AF XY: 0.275 AC XY: 20410 AN XY: 74282

African (AFR) AF: 0.241 AC: 10008 AN: 41442

American (AMR) AF: 0.325 AC: 4955 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3468

East Asian (EAS) AF: 0.192 AC: 995 AN: 5194

South Asian (SAS) AF: 0.245 AC: 1179 AN: 4804

European-Finnish (FIN) AF: 0.262 AC: 2760 AN: 10550

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20390 AN: 67962

Other (OTH) AF: 0.302 AC: 636 AN: 2108

Alfa AF: 0.293 Hom.: 21475

Bravo AF: 0.282

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10086908; hg19: chr8-128011937;