rs6470518

Variant names:

• chr8-127471936-G-A
• rs6470518
• ENST00000502056.1:n.1041+7147C>T

Variant summary

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

The ENST00000502056.1(CASC8):​n.1041+7147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,036 control chromosomes in the GnomAD database, including 57,902 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 0.87 (57902 hom., cov: 30)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.10
• 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC8	NR_024393.1	n.1041+7147C>T		intron_variant	Intron 4 of 4
CASC8	NR_117100.1	n.1041+7147C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC8	ENST00000502056.1	n.1041+7147C>T		intron_variant	Intron 4 of 4	1
CASC8	ENST00000502082.5	n.1041+7147C>T		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132421 AN: 151918 Hom.: 57867 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.872 AC: 132508 AN: 152036 Hom.: 57902 Cov.: 30 AF XY: 0.869 AC XY: 64594 AN XY: 74332

African (AFR) AF: 0.817 AC: 33864 AN: 41424

American (AMR) AF: 0.913 AC: 13951 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3263 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4389 AN: 5162

South Asian (SAS) AF: 0.874 AC: 4204 AN: 4812

European-Finnish (FIN) AF: 0.825 AC: 8724 AN: 10570

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61138 AN: 67992

Other (OTH) AF: 0.884 AC: 1871 AN: 2116

Alfa AF: 0.911 Hom.: 10967

Bravo AF: 0.873

Asia WGS AF: 0.810 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.068
DANN	Benign	0.36
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs6470518; hg19: chr8-128484181;