8-127119546-C-G

Variant names:

• chr8-127119546-C-G
• rs10098156
• ENST00000641912.1:n.879-2581G>C

Variant summary

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

The ENST00000641912.1(CASC19):​n.879-2581G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,246 control chromosomes in the GnomAD database, including 59,109 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 0.88 (59109 hom., cov: 32)
• Consequence: CASC19 ENST00000641912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641912.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC19	ENST00000641912.1		n.879-2581G>C		intron	N/A
	CASC19	ENST00000641919.1		n.869-2581G>C		intron	N/A
	CASC19	ENST00000642100.1		n.418-40413G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133908 AN: 152128 Hom.: 59070 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.880 AC: 134003 AN: 152246 Hom.: 59109 Cov.: 32 AF XY: 0.876 AC XY: 65182 AN XY: 74438

African (AFR) AF: 0.901 AC: 37440 AN: 41570

American (AMR) AF: 0.830 AC: 12682 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2837 AN: 3472

East Asian (EAS) AF: 0.972 AC: 5043 AN: 5188

South Asian (SAS) AF: 0.862 AC: 4151 AN: 4814

European-Finnish (FIN) AF: 0.833 AC: 8818 AN: 10586

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.884 AC: 60109 AN: 68012

Other (OTH) AF: 0.879 AC: 1859 AN: 2116

Alfa AF: 0.891 Hom.: 7527

Bravo AF: 0.879

Asia WGS AF: 0.903 AC: 3139 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.40
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10098156; hg19: chr8-128131791;