8-126769195-T-G

Variant names:

• chr8-126769195-T-G
• rs12543473
• ENST00000520224.2:n.714+205A>C

Variant summary

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

The ENST00000520224.2(ENSG00000253573):​n.714+205A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,050 control chromosomes in the GnomAD database, including 10,825 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 0.28 (10825 hom., cov: 32)
• Consequence: ENSG00000253573 ENST00000520224.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 2 publications found

Genes affected

ENSG00000253573 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520224.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375751	NR_188069.1		n.544+55521T>G		intron	N/A
	LOC105375751	NR_188070.1		n.545-24586T>G		intron	N/A
	LOC105375751	NR_188071.1		n.735-24586T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253573	ENST00000520224.2	TSL:3	n.714+205A>C		intron	N/A
	PCAT1	ENST00000645198.1		n.21+55521T>G		intron	N/A
	PCAT1	ENST00000645463.1		n.672+55521T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43125 AN: 151932 Hom.: 10767 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0957

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.284 AC: 43250 AN: 152050 Hom.: 10825 Cov.: 32 AF XY: 0.282 AC XY: 20952 AN XY: 74322

African (AFR) AF: 0.668 AC: 27660 AN: 41414

American (AMR) AF: 0.306 AC: 4682 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5164

South Asian (SAS) AF: 0.148 AC: 713 AN: 4822

European-Finnish (FIN) AF: 0.0957 AC: 1013 AN: 10590

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6591 AN: 67994

Other (OTH) AF: 0.257 AC: 541 AN: 2104

Alfa AF: 0.157 Hom.: 9811

Bravo AF: 0.318

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.72
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs12543473; hg19: chr8-127781440;