rs7001069

Variant names:

• chr8-127098401-A-G
• rs7001069
• ENST00000642100.1:n.418-19268T>C

Variant summary

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

The ENST00000642100.1(CASC19):​n.418-19268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,092 control chromosomes in the GnomAD database, including 2,596 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 0.13 (2596 hom., cov: 32)
• Consequence: CASC19 ENST00000642100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 10 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642100.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC19	ENST00000642100.1		n.418-19268T>C		intron	N/A
	PCAT1	ENST00000645463.1		n.855+91783A>G		intron	N/A
	PCAT1	ENST00000646670.1		n.1064+84627A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19195 AN: 151974 Hom.: 2585 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.127 AC: 19245 AN: 152092 Hom.: 2596 Cov.: 32 AF XY: 0.125 AC XY: 9312 AN XY: 74344

African (AFR) AF: 0.328 AC: 13596 AN: 41424

American (AMR) AF: 0.0554 AC: 846 AN: 15282

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

East Asian (EAS) AF: 0.244 AC: 1264 AN: 5178

South Asian (SAS) AF: 0.101 AC: 488 AN: 4816

European-Finnish (FIN) AF: 0.0510 AC: 540 AN: 10590

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0319 AC: 2172 AN: 68012

Other (OTH) AF: 0.0895 AC: 189 AN: 2112

Alfa AF: 0.0663 Hom.: 516

Bravo AF: 0.135

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.29
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7001069; hg19: chr8-128110646;