8-127427922-C-A

Variant names:

• chr8-127427922-C-A
• rs9297756
• ENST00000502082.5:n.1042-6959G>T

Variant summary

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

The ENST00000502082.5(CASC8):​n.1042-6959G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,180 control chromosomes in the GnomAD database, including 2,236 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 0.17 (2236 hom., cov: 33)
• Consequence: CASC8 ENST00000502082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 9 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502082.5. 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
	CASC8	NR_117100.1		n.1042-6959G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502082.5	TSL:1	n.1042-6959G>T		intron	N/A
	CASC8	ENST00000842817.1		n.82-6959G>T		intron	N/A
	CASC8	ENST00000842818.1		n.138-6959G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25392 AN: 152062 Hom.: 2236 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.167 AC: 25390 AN: 152180 Hom.: 2236 Cov.: 33 AF XY: 0.169 AC XY: 12609 AN XY: 74406

African (AFR) AF: 0.188 AC: 7811 AN: 41498

American (AMR) AF: 0.127 AC: 1938 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1101 AN: 5184

South Asian (SAS) AF: 0.111 AC: 536 AN: 4826

European-Finnish (FIN) AF: 0.225 AC: 2387 AN: 10590

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10328 AN: 68002

Other (OTH) AF: 0.173 AC: 365 AN: 2112

Alfa AF: 0.153 Hom.: 6980

Bravo AF: 0.162

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.65
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9297756; hg19: chr8-128440167;