rs16902094

Variant names:

• chr8-127308101-A-G
• rs16902094
• ENST00000501396.6:n.686+14914T>C

Variant summary

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

The ENST00000501396.6(CASC8):​n.686+14914T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,224 control chromosomes in the GnomAD database, including 1,827 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 0.15 (1827 hom., cov: 33)
• Consequence: CASC8 ENST00000501396.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 92 publications found

Genes affected

CASC8 (HGNC:45129): (cancer susceptibility 8)

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]

CASC21 (HGNC:49836): (cancer susceptibility 21)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000501396.6. 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
	CASC21	NR_117099.1		n.149-13972A>G		intron	N/A
	CASC8	NR_117100.1		n.1177-18041T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000501396.6	TSL:1	n.686+14914T>C		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1177-18041T>C		intron	N/A
	CASC8	ENST00000523825.3	TSL:1	n.547-18041T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22705 AN: 152106 Hom.: 1825 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.149 AC: 22723 AN: 152224 Hom.: 1827 Cov.: 33 AF XY: 0.157 AC XY: 11679 AN XY: 74418

African (AFR) AF: 0.117 AC: 4856 AN: 41558

American (AMR) AF: 0.158 AC: 2423 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5174

South Asian (SAS) AF: 0.168 AC: 813 AN: 4826

European-Finnish (FIN) AF: 0.242 AC: 2562 AN: 10574

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9990 AN: 68004

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.144 Hom.: 5372

Bravo AF: 0.139

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.61
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs16902094; hg19: chr8-128320346;