chr8-127454569-C-T

Variant names:

• chr8-127454569-C-T
• rs7841264
• ENST00000502056.1:n.1042-10849G>A

Variant summary

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

The ENST00000502056.1(CASC8):​n.1042-10849G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,108 control chromosomes in the GnomAD database, including 3,830 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 0.21 (3830 hom., cov: 33)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 12 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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.1042-10849G>A		intron	N/A
	CASC8	NR_117100.1		n.1041+24514G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1042-10849G>A		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+24514G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31763 AN: 151990 Hom.: 3819 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.209 AC: 31787 AN: 152108 Hom.: 3830 Cov.: 33 AF XY: 0.216 AC XY: 16037 AN XY: 74362

African (AFR) AF: 0.173 AC: 7193 AN: 41492

American (AMR) AF: 0.327 AC: 4998 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2695 AN: 5182

South Asian (SAS) AF: 0.237 AC: 1141 AN: 4820

European-Finnish (FIN) AF: 0.215 AC: 2275 AN: 10574

Middle Eastern (MID) AF: 0.193 AC: 56 AN: 290

European-Non Finnish (NFE) AF: 0.181 AC: 12316 AN: 67972

Other (OTH) AF: 0.215 AC: 454 AN: 2108

Alfa AF: 0.191 Hom.: 13252

Bravo AF: 0.215

Asia WGS AF: 0.345 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.42
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7841264; hg19: chr8-128466814;