rs4345522

Variant names:

• chr8-126575129-C-T
• rs4345522
• ENST00000517773.6:n.447-14063C>T

Variant summary

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

The ENST00000517773.6(PCAT1):​n.447-14063C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,070 control chromosomes in the GnomAD database, including 11,257 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 0.36 (11257 hom., cov: 33)
• Consequence: PCAT1 ENST00000517773.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.57-14063C>T		intron_variant	Intron 1 of 5
LOC105375751	NR_188070.1	n.57-14063C>T		intron_variant	Intron 1 of 3
LOC105375751	NR_188071.1	n.57-14063C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000517773.6	n.447-14063C>T		intron_variant	Intron 1 of 2	3
PCAT1	ENST00000517915.3	n.110-14063C>T		intron_variant	Intron 1 of 2	3
PCAT1	ENST00000519880.5	n.58-14063C>T		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.355 AC: 54010 AN: 151952 Hom.: 11223 Cov.: 33

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.356 AC: 54110 AN: 152070 Hom.: 11257 Cov.: 33 AF XY: 0.358 AC XY: 26605 AN XY: 74342

African (AFR) AF: 0.558 AC: 23116 AN: 41442

American (AMR) AF: 0.371 AC: 5661 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3231 AN: 5184

South Asian (SAS) AF: 0.275 AC: 1328 AN: 4824

European-Finnish (FIN) AF: 0.265 AC: 2796 AN: 10568

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16223 AN: 67992

Other (OTH) AF: 0.323 AC: 681 AN: 2110

Alfa AF: 0.277 Hom.: 3536

Bravo AF: 0.377

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.044
DANN	Benign	0.45
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4345522; hg19: chr8-127587374;