ENST00000642100.1:n.418-33817G>A

Variant names:

• chr8-127112950-C-T
• rs10505483
• ENST00000642100.1:n.418-33817G>A

Variant summary

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

The ENST00000642100.1(CASC19):​n.418-33817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,006 control chromosomes in the GnomAD database, including 4,306 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 0.16 (4306 hom., cov: 32)
• Consequence: CASC19 ENST00000642100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 36 publications found

Genes affected

CASC19 (HGNC:49476): (cancer susceptibility 19)

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000642100.1	n.418-33817G>A		intron_variant	Intron 1 of 1
PCAT1	ENST00000645463.1	n.855+106332C>T		intron_variant	Intron 6 of 6
PCAT1	ENST00000646670.1	n.1064+99176C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23874 AN: 151888 Hom.: 4287 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0514

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.158 AC: 23943 AN: 152006 Hom.: 4306 Cov.: 32 AF XY: 0.155 AC XY: 11522 AN XY: 74308

African (AFR) AF: 0.435 AC: 18033 AN: 41410

American (AMR) AF: 0.0668 AC: 1021 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1267 AN: 5174

South Asian (SAS) AF: 0.102 AC: 492 AN: 4814

European-Finnish (FIN) AF: 0.0514 AC: 542 AN: 10552

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2195 AN: 67990

Other (OTH) AF: 0.114 AC: 241 AN: 2110

Alfa AF: 0.0762 Hom.: 5061

Bravo AF: 0.170

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10505483; hg19: chr8-128125195;