chr8-126911475-C-T

Variant names:

• chr8-126911475-C-T
• rs979200
• ENST00000519319.2:n.262+32995C>T

Variant summary

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

The ENST00000519319.2(PCAT1):​n.262+32995C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,070 control chromosomes in the GnomAD database, including 16,767 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 0.45 (16767 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 9 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.663+33685C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.262+32995C>T		intron_variant	Intron 3 of 4	2
PCAT1	ENST00000643079.1	n.9+32995C>T		intron_variant	Intron 1 of 3
PCAT1	ENST00000643101.1	n.161+33685C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67890 AN: 151952 Hom.: 16751 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.447 AC: 67940 AN: 152070 Hom.: 16767 Cov.: 32 AF XY: 0.441 AC XY: 32768 AN XY: 74320

African (AFR) AF: 0.663 AC: 27509 AN: 41486

American (AMR) AF: 0.406 AC: 6204 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3462

East Asian (EAS) AF: 0.495 AC: 2562 AN: 5176

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4824

European-Finnish (FIN) AF: 0.280 AC: 2955 AN: 10552

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24393 AN: 67962

Other (OTH) AF: 0.465 AC: 983 AN: 2112

Alfa AF: 0.387 Hom.: 23825

Bravo AF: 0.472

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.61
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs979200; hg19: chr8-127923720;