rs16902094

Positions:

• chr8-127308101-A-G

Variant summary

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

The ENST00000501396.5(CASC8):​n.686+14914T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,224 control chromosomes in the GnomAD database, including 1,827 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 0.15 (1827 hom., cov: 33)
• Consequence: CASC8 ENST00000501396.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396

Genes affected

CASC8 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC21	NR_117099.1	n.149-13972A>G		intron_variant
CASC8	NR_117100.1	n.1177-18041T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC8	ENST00000501396.5	n.686+14914T>C		intron_variant		1
CASC8	ENST00000502082.5	n.1177-18041T>C		intron_variant		1
CASC8	ENST00000523825.2	n.547-18041T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22705 AN: 152106 Hom.: 1825 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.149 AC: 22723 AN: 152224 Hom.: 1827 Cov.: 33 AF XY: 0.157 AC XY: 11679 AN XY: 74418

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.131

Alfa AF: 0.146 Hom.: 2329

Bravo AF: 0.139

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16902094; hg19: chr8-128320346;