rs4871799

chr8-127470397-G-Achr8-127470397-G-C

Variant summary

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

The NR_117100.1(CASC8):n.1041+8686C>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 0.7 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 NR_117100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC8	NR_117100.1	n.1041+8686C>T		intron_variant, non_coding_transcript_variant
CASC8	NR_024393.1	n.1041+8686C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC8	ENST00000502056.1	n.1041+8686C>T		intron_variant, non_coding_transcript_variant		1
CASC8	ENST00000502082.5	n.1041+8686C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.716

Alfa AF: 0.757 Hom.: 85820

Bravo AF: 0.697

Asia WGS AF: 0.657 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.45
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871799; hg19: chr8-128482642;