8-127463572-G-A

Variant names:

• chr8-127463572-G-A
• rs7825118
• ENST00000502056.1:n.1041+15511C>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+15511C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,130 control chromosomes in the GnomAD database, including 3,741 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 0.20 (3741 hom., cov: 31)
• Consequence: CASC8 ENST00000502056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 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+15511C>T		intron	N/A
	CASC8	NR_117100.1		n.1041+15511C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC8	ENST00000502056.1	TSL:1	n.1041+15511C>T		intron	N/A
	CASC8	ENST00000502082.5	TSL:1	n.1041+15511C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31176 AN: 152014 Hom.: 3742 Cov.: 31

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.205 AC: 31170 AN: 152130 Hom.: 3741 Cov.: 31 AF XY: 0.208 AC XY: 15439 AN XY: 74342

African (AFR) AF: 0.0864 AC: 3589 AN: 41550

American (AMR) AF: 0.285 AC: 4357 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1189 AN: 5160

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2812 AN: 10536

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16280 AN: 67994

Other (OTH) AF: 0.223 AC: 471 AN: 2108

Alfa AF: 0.221 Hom.: 6952

Bravo AF: 0.206

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.59
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7825118; hg19: chr8-128475817;