rs4871799

Variant names:

• chr8-127470397-G-A
• rs4871799
• ENST00000502056.1:n.1041+8686C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-127470397-G-A
• chr8-127470397-G-C

Variant summary

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

The ENST00000502056.1(CASC8):​n.1041+8686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,172 control chromosomes in the GnomAD database, including 37,869 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 0.70 (37869 hom., cov: 32)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 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+8686C>T		intron	N/A
	CASC8	NR_117100.1		n.1041+8686C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1041+8686C>T		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+8686C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106491 AN: 152054 Hom.: 37873 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.700 AC: 106519 AN: 152172 Hom.: 37869 Cov.: 32 AF XY: 0.698 AC XY: 51914 AN XY: 74372

African (AFR) AF: 0.574 AC: 23828 AN: 41512

American (AMR) AF: 0.736 AC: 11261 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2715 AN: 3472

East Asian (EAS) AF: 0.630 AC: 3256 AN: 5170

South Asian (SAS) AF: 0.774 AC: 3732 AN: 4824

European-Finnish (FIN) AF: 0.676 AC: 7143 AN: 10574

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52095 AN: 68008

Other (OTH) AF: 0.716 AC: 1513 AN: 2112

Alfa AF: 0.745 Hom.: 131274

Bravo AF: 0.697

Asia WGS AF: 0.657 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.94
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4871799; hg19: chr8-128482642;