rs10099905

Variant names:

• chr8-127455689-A-C
• rs10099905
• ENST00000502056.1:n.1042-11969T>G

Variant summary

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

The ENST00000502056.1(CASC8):​n.1042-11969T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,090 control chromosomes in the GnomAD database, including 47,945 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 0.79 (47945 hom., cov: 31)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502056.1. 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
	CASC8	NR_024393.1		n.1042-11969T>G		intron	N/A
	CASC8	NR_117100.1		n.1041+23394T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1042-11969T>G		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+23394T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120530 AN: 151972 Hom.: 47900 Cov.: 31

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.793 AC: 120637 AN: 152090 Hom.: 47945 Cov.: 31 AF XY: 0.797 AC XY: 59220 AN XY: 74344

African (AFR) AF: 0.766 AC: 31757 AN: 41466

American (AMR) AF: 0.764 AC: 11669 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3470

East Asian (EAS) AF: 0.853 AC: 4404 AN: 5160

South Asian (SAS) AF: 0.843 AC: 4062 AN: 4816

European-Finnish (FIN) AF: 0.874 AC: 9254 AN: 10584

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54062 AN: 68004

Other (OTH) AF: 0.810 AC: 1711 AN: 2112

Alfa AF: 0.788 Hom.: 73283

Bravo AF: 0.778

Asia WGS AF: 0.853 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.37
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10099905; hg19: chr8-128467934;