rs6470519

Variant names:

• chr8-127471978-A-C
• rs6470519
• ENST00000502056.1:n.1041+7105T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-127471978-A-C
• chr8-127471978-A-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+7105T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,098 control chromosomes in the GnomAD database, including 57,930 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 (57930 hom., cov: 31)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 9 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.9 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.1041+7105T>G		intron	N/A
	CASC8	NR_117100.1		n.1041+7105T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1041+7105T>G		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+7105T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132459 AN: 151982 Hom.: 57897 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.871 AC: 132543 AN: 152098 Hom.: 57930 Cov.: 31 AF XY: 0.869 AC XY: 64574 AN XY: 74324

African (AFR) AF: 0.817 AC: 33873 AN: 41456

American (AMR) AF: 0.912 AC: 13954 AN: 15296

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

East Asian (EAS) AF: 0.851 AC: 4403 AN: 5176

South Asian (SAS) AF: 0.873 AC: 4207 AN: 4818

European-Finnish (FIN) AF: 0.825 AC: 8716 AN: 10566

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61152 AN: 67994

Other (OTH) AF: 0.883 AC: 1869 AN: 2116

Alfa AF: 0.896 Hom.: 95585

Bravo AF: 0.873

Asia WGS AF: 0.809 AC: 2814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		-0.20

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: rs6470519;

hg19: chr8-128484223;