rs4871798

chr8-127467718-T-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+11365A>G 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 0.791 in 152,134 control chromosomes in the GnomAD database, including 48,268 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 0.79 (48268 hom., cov: 33)
• Consequence: CASC8 NR_117100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC8	NR_117100.1	n.1041+11365A>G		intron_variant, non_coding_transcript_variant
CASC8	NR_024393.1	n.1041+11365A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC8	ENST00000502056.1	n.1041+11365A>G		intron_variant, non_coding_transcript_variant		1
CASC8	ENST00000502082.5	n.1041+11365A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120239 AN: 152016 Hom.: 48270 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.791 AC: 120271 AN: 152134 Hom.: 48268 Cov.: 33 AF XY: 0.788 AC XY: 58589 AN XY: 74348

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.827

Alfa AF: 0.858 Hom.: 60481

Bravo AF: 0.785

Asia WGS AF: 0.722 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.0
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871798; hg19: chr8-128479963;