rs7830412

chr8-127458796-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_117100.1(CASC8):n.1041+20287C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 152,200 control chromosomes in the GnomAD database, including 201 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 0.051 (201 hom., cov: 32)
• Consequence: CASC8 NR_117100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

Genes affected

CASC8 (HGNC:45129): (cancer susceptibility 8)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC8	NR_117100.1	n.1041+20287C>T		intron_variant, non_coding_transcript_variant
CASC8	NR_024393.1	n.1042-15076C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC8	ENST00000502056.1	n.1042-15076C>T		intron_variant, non_coding_transcript_variant		1
CASC8	ENST00000502082.5	n.1041+20287C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0505 AC: 7686 AN: 152082 Hom.: 200 Cov.: 32

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0582

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0506 AC: 7697 AN: 152200 Hom.: 201 Cov.: 32 AF XY: 0.0514 AC XY: 3820 AN XY: 74390

Gnomad4 AFR AF: 0.0466

Gnomad4 AMR AF: 0.0669

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.0338

Gnomad4 FIN AF: 0.0582

Gnomad4 NFE AF: 0.0483

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0515 Hom.: 305

Bravo AF: 0.0532

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7830412; hg19: chr8-128471041;