rs10094871

Variant names:

• chr8-127459724-A-G
• rs10094871
• ENST00000502056.1:n.1042-16004T>C

Variant summary

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

The ENST00000502056.1(CASC8):​n.1042-16004T>C variant causes a intron 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 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608
• Publications: 6 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 = 0.185 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.1042-16004T>C		intron	N/A
	CASC8	NR_117100.1		n.1041+19359T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1042-16004T>C		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+19359T>C		intron	N/A

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

African (AFR) AF: 0.0979 AC: 4069 AN: 41550

American (AMR) AF: 0.140 AC: 2149 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1011 AN: 5192

South Asian (SAS) AF: 0.120 AC: 578 AN: 4828

European-Finnish (FIN) AF: 0.153 AC: 1627 AN: 10600

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12084 AN: 68000

Other (OTH) AF: 0.167 AC: 353 AN: 2112

Alfa AF: 0.169 Hom.: 2061

Bravo AF: 0.149

Asia WGS AF: 0.148 AC: 516 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.61
PhyloP100		0.61

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: rs10094871;

hg19: chr8-128471969;