rs16901896

Variant names:

• chr8-126998523-A-G
• rs16901896
• ENST00000519319.2:n.263-8032A>G

Variant summary

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

The ENST00000519319.2(PCAT1):​n.263-8032A>G variant causes a intron 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 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 8 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=-0.87).
• 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 rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.664-8032A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.263-8032A>G		intron_variant	Intron 3 of 4	2
PCAT1	ENST00000643079.1	n.10-8032A>G		intron_variant	Intron 1 of 3
PCAT1	ENST00000643101.1	n.162-8032A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0628 AC: 2610 AN: 41564

American (AMR) AF: 0.138 AC: 2116 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1661 AN: 5176

South Asian (SAS) AF: 0.0454 AC: 219 AN: 4824

European-Finnish (FIN) AF: 0.0921 AC: 976 AN: 10602

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0785 AC: 5340 AN: 68014

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.0833 Hom.: 1125

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
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16901896; hg19: chr8-128010768;