rs7825118

Positions:

• chr8-127463572-G-A
• chr8-127463572-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CASC8 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC8	NR_024393.1	n.1041+15511C>T		intron_variant
CASC8	NR_117100.1	n.1041+15511C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC8	ENST00000502056.1	n.1041+15511C>T		intron_variant		1
CASC8	ENST00000502082.5	n.1041+15511C>T		intron_variant		1

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

Gnomad4 AFR AF: 0.0864

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.223

Alfa AF: 0.210 Hom.: 1626

Bravo AF: 0.206

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7825118; hg19: chr8-128475817;