rs10094059

chr8-127449362-C-Gchr8-127449362-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_117100.1(CASC8):n.1042-28399G>C variant causes a intron, non coding transcript 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 NR_117100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC8	NR_117100.1	n.1042-28399G>C		intron_variant, non_coding_transcript_variant
CASC8	NR_024393.1	n.1042-5642G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC8	ENST00000502056.1	n.1042-5642G>C		intron_variant, non_coding_transcript_variant		1
CASC8	ENST00000502082.5	n.1042-28399G>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.739

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10094059; hg19: chr8-128461607;