rs10096900

Variant names:

• chr8-127696039-C-A
• rs10096900
• ENST00000502463.7:n.144-4173G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-127696039-C-A
• chr8-127696039-C-G
• chr8-127696039-C-T

Variant summary

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

The ENST00000502463.7(CASC11):​n.144-4173G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,036 control chromosomes in the GnomAD database, including 8,732 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 0.34 (8732 hom., cov: 32)
• Consequence: CASC11 ENST00000502463.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556

Genes affected

CASC11 (HGNC:48939): (cancer susceptibility 11)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC11	ENST00000502463.7	n.144-4173G>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51100 AN: 151916 Hom.: 8710 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.337 AC: 51166 AN: 152036 Hom.: 8732 Cov.: 32 AF XY: 0.335 AC XY: 24893 AN XY: 74316

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.353

Alfa AF: 0.332 Hom.: 9384

Bravo AF: 0.347

Asia WGS AF: 0.278 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10096900; hg19: chr8-128708284;