chr8-127459431-C-T

Variant names:

• chr8-127459431-C-T
• rs4871023
• ENST00000502056.1:n.1042-15711G>A

Variant summary

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

The ENST00000502056.1(CASC8):​n.1042-15711G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0244 in 151,080 control chromosomes in the GnomAD database, including 75 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 0.024 (75 hom., cov: 32)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0961 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.1042-15711G>A		intron	N/A
	CASC8	NR_117100.1		n.1041+19652G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1042-15711G>A		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+19652G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0243 AC: 3676 AN: 151040 Hom.: 74 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0376

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0161

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0173

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

GnomAD4 genome AF: 0.0244 AC: 3687 AN: 151080 Hom.: 75 Cov.: 32 AF XY: 0.0269 AC XY: 1981 AN XY: 73660

African (AFR) AF: 0.0187 AC: 769 AN: 41134

American (AMR) AF: 0.0491 AC: 746 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3466

East Asian (EAS) AF: 0.103 AC: 533 AN: 5156

South Asian (SAS) AF: 0.0378 AC: 180 AN: 4768

European-Finnish (FIN) AF: 0.0428 AC: 436 AN: 10186

Middle Eastern (MID) AF: 0.0176 AC: 5 AN: 284

European-Non Finnish (NFE) AF: 0.0142 AC: 967 AN: 67886

Other (OTH) AF: 0.0182 AC: 38 AN: 2088

Alfa AF: 0.0172 Hom.: 60

Bravo AF: 0.0257

Asia WGS AF: 0.0740 AC: 256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.20
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs4871023; hg19: chr8-128471676;