rs10094059

Variant names:

• chr8-127449362-C-G
• rs10094059
• ENST00000502056.1:n.1042-5642G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-127449362-C-G
• chr8-127449362-C-T

Variant summary

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

The ENST00000502056.1(CASC8):​n.1042-5642G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,054 control chromosomes in the GnomAD database, including 40,180 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 0.72 (40180 hom., cov: 31)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	NR_024393.1		n.1042-5642G>C		intron	N/A
	CASC8	NR_117100.1		n.1042-28399G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1042-5642G>C		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1042-28399G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109759 AN: 151936 Hom.: 40167 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.722 AC: 109817 AN: 152054 Hom.: 40180 Cov.: 31 AF XY: 0.724 AC XY: 53820 AN XY: 74334

African (AFR) AF: 0.619 AC: 25663 AN: 41434

American (AMR) AF: 0.722 AC: 11029 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2802 AN: 3468

East Asian (EAS) AF: 0.898 AC: 4647 AN: 5174

South Asian (SAS) AF: 0.637 AC: 3071 AN: 4820

European-Finnish (FIN) AF: 0.830 AC: 8787 AN: 10590

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51323 AN: 67972

Other (OTH) AF: 0.739 AC: 1560 AN: 2110

Alfa AF: 0.703 Hom.: 2541

Bravo AF: 0.710

Asia WGS AF: 0.757 AC: 2633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.51
PhyloP100		0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10094059;

hg19: chr8-128461607;