rs10094871

chr8-127459724-A-G

Variant summary

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

The NR_117100.1(CASC8):n.1041+19359T>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 0.152 in 152,264 control chromosomes in the GnomAD database, including 1,928 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 (1928 hom., cov: 32)
• Consequence: CASC8 NR_117100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

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 = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC8	NR_117100.1	n.1041+19359T>C		intron_variant, non_coding_transcript_variant
CASC8	NR_024393.1	n.1042-16004T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC8	ENST00000502056.1	n.1042-16004T>C		intron_variant, non_coding_transcript_variant		1
CASC8	ENST00000502082.5	n.1041+19359T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23054 AN: 152146 Hom.: 1924 Cov.: 32

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.151 AC: 23068 AN: 152264 Hom.: 1928 Cov.: 32 AF XY: 0.149 AC XY: 11092 AN XY: 74448

Gnomad4 AFR AF: 0.0979

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.167

Alfa AF: 0.165 Hom.: 1120

Bravo AF: 0.149

Asia WGS AF: 0.148 AC: 516 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.6
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10094871; hg19: chr8-128471969;