ENST00000502056.1:n.1041+6290T>G

Variant names:

• chr8-127472793-A-C
• rs1447295
• ENST00000502056.1:n.1041+6290T>G

Variant summary

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

The ENST00000502056.1(CASC8):​n.1041+6290T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 151,384 control chromosomes in the GnomAD database, including 53,028 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 0.83 (53028 hom., cov: 28)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 273 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 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.1041+6290T>G		intron	N/A
	CASC8	NR_117100.1		n.1041+6290T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1041+6290T>G		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+6290T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.831 AC: 125773 AN: 151266 Hom.: 53012 Cov.: 28

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.831 AC: 125832 AN: 151384 Hom.: 53028 Cov.: 28 AF XY: 0.830 AC XY: 61351 AN XY: 73890

African (AFR) AF: 0.679 AC: 27927 AN: 41146

American (AMR) AF: 0.896 AC: 13585 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3260 AN: 3466

East Asian (EAS) AF: 0.844 AC: 4350 AN: 5156

South Asian (SAS) AF: 0.870 AC: 4145 AN: 4762

European-Finnish (FIN) AF: 0.824 AC: 8629 AN: 10474

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61044 AN: 67916

Other (OTH) AF: 0.855 AC: 1793 AN: 2096

Alfa AF: 0.881 Hom.: 257343

Bravo AF: 0.827

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.52
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1447295; hg19: chr8-128485038;