rs16901896

chr8-126998523-A-G

Variant summary

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

The ENST00000645463.1(PCAT1):n.792-8032A>G 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 0.089 in 152,270 control chromosomes in the GnomAD database, including 824 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 0.089 (824 hom., cov: 32)
• Consequence: PCAT1 ENST00000645463.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375751	XR_007061105.1	n.1734+7652A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCAT1	ENST00000645463.1	n.792-8032A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0890 AC: 13549 AN: 152152 Hom.: 827 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0890 AC: 13546 AN: 152270 Hom.: 824 Cov.: 32 AF XY: 0.0903 AC XY: 6724 AN XY: 74440

Gnomad4 AFR AF: 0.0628

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0921

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0810 Hom.: 726

Bravo AF: 0.0957

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.14
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16901896; hg19: chr8-128010768;