8-126913383-T-A

Variant names:

• chr8-126913383-T-A
• rs7839365
• ENST00000519319.2:n.262+34903T>A

Variant summary

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

The ENST00000519319.2(PCAT1):​n.262+34903T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,022 control chromosomes in the GnomAD database, including 12,260 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 0.40 (12260 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.663+35593T>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.262+34903T>A		intron_variant	Intron 3 of 4	2
PCAT1	ENST00000643079.1	n.9+34903T>A		intron_variant	Intron 1 of 3
PCAT1	ENST00000643101.1	n.161+35593T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60470 AN: 151904 Hom.: 12243 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.398 AC: 60514 AN: 152022 Hom.: 12260 Cov.: 32 AF XY: 0.403 AC XY: 29976 AN XY: 74296

African (AFR) AF: 0.381 AC: 15790 AN: 41482

American (AMR) AF: 0.461 AC: 7047 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2184 AN: 5162

South Asian (SAS) AF: 0.362 AC: 1745 AN: 4814

European-Finnish (FIN) AF: 0.450 AC: 4742 AN: 10548

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.388 AC: 26359 AN: 67964

Other (OTH) AF: 0.392 AC: 826 AN: 2108

Alfa AF: 0.381 Hom.: 1407

Bravo AF: 0.402

Asia WGS AF: 0.374 AC: 1298 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.76
DANN	Benign	0.86
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7839365; hg19: chr8-127925628;