chr8-127113604-A-G

Variant names:

• chr8-127113604-A-G
• rs10505482
• ENST00000642100.1:n.418-34471T>C

Variant summary

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

The ENST00000642100.1(CASC19):​n.418-34471T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,060 control chromosomes in the GnomAD database, including 4,729 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 0.24 (4729 hom., cov: 32)
• Consequence: CASC19 ENST00000642100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC19	ENST00000642100.1		n.418-34471T>C		intron	N/A
	PCAT1	ENST00000645463.1		n.855+106986A>G		intron	N/A
	PCAT1	ENST00000646670.1		n.1064+99830A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36302 AN: 151940 Hom.: 4732 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.239 AC: 36299 AN: 152060 Hom.: 4729 Cov.: 32 AF XY: 0.243 AC XY: 18097 AN XY: 74334

African (AFR) AF: 0.140 AC: 5794 AN: 41492

American (AMR) AF: 0.231 AC: 3529 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3466

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2152 AN: 4810

European-Finnish (FIN) AF: 0.259 AC: 2732 AN: 10566

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19048 AN: 67970

Other (OTH) AF: 0.243 AC: 513 AN: 2114

Alfa AF: 0.241 Hom.: 3079

Bravo AF: 0.225

Asia WGS AF: 0.302 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.43
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs10505482; hg19: chr8-128125849;