rs4345522

chr8-126575129-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645463.1(PCAT1):n.40-14063C>T variant causes a intron, non coding transcript 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 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375751	XR_007061097.1	n.1388+17198C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.40-14063C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.323

Alfa AF: 0.280 Hom.: 3291

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4345522; hg19: chr8-127587374;