rs4871005

Variant names:

• chr8-127001131-A-C
• rs4871005
• ENST00000519319.2:n.263-5424A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-127001131-A-C
• chr8-127001131-A-G
• chr8-127001131-A-T

Variant summary

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

The ENST00000519319.2(PCAT1):​n.263-5424A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,022 control chromosomes in the GnomAD database, including 22,683 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 0.53 (22683 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.664-5424A>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.263-5424A>C		intron_variant	Intron 3 of 4	2
PCAT1	ENST00000643079.1	n.10-5424A>C		intron_variant	Intron 1 of 3
PCAT1	ENST00000643101.1	n.162-5424A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80528 AN: 151904 Hom.: 22665 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.530 AC: 80580 AN: 152022 Hom.: 22683 Cov.: 32 AF XY: 0.538 AC XY: 39975 AN XY: 74308

African (AFR) AF: 0.321 AC: 13312 AN: 41470

American (AMR) AF: 0.599 AC: 9149 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1860 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3188 AN: 5174

South Asian (SAS) AF: 0.588 AC: 2835 AN: 4820

European-Finnish (FIN) AF: 0.655 AC: 6916 AN: 10560

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41332 AN: 67944

Other (OTH) AF: 0.556 AC: 1174 AN: 2112

Alfa AF: 0.580 Hom.: 83104

Bravo AF: 0.519

Asia WGS AF: 0.602 AC: 2091 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.69
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4871005; hg19: chr8-128013376;