rs10808550

Variant names:

• chr8-126610205-A-G
• rs10808550
• ENST00000517773.6:n.546-7184A>G

Variant summary

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

The ENST00000517773.6(PCAT1):​n.546-7184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,240 control chromosomes in the GnomAD database, including 2,817 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 0.19 (2817 hom., cov: 33)
• Consequence: PCAT1 ENST00000517773.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.155+20915A>G		intron_variant	Intron 2 of 5
LOC105375751	NR_188070.1	n.155+20915A>G		intron_variant	Intron 2 of 3
LOC105375751	NR_188071.1	n.155+20915A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000517773.6	n.546-7184A>G		intron_variant	Intron 2 of 2	3
PCAT1	ENST00000517915.3	n.208+20915A>G		intron_variant	Intron 2 of 2	3
PCAT1	ENST00000519880.5	n.156+20915A>G		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28198 AN: 152122 Hom.: 2785 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.186 AC: 28267 AN: 152240 Hom.: 2817 Cov.: 33 AF XY: 0.184 AC XY: 13704 AN XY: 74448

African (AFR) AF: 0.230 AC: 9562 AN: 41520

American (AMR) AF: 0.171 AC: 2611 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1291 AN: 5186

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4820

European-Finnish (FIN) AF: 0.0896 AC: 952 AN: 10622

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11120 AN: 68014

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.175 Hom.: 322

Bravo AF: 0.191

Asia WGS AF: 0.299 AC: 1041 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	0.10
DANN	Benign	0.65
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10808550; hg19: chr8-127622450;