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. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502463.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	ENST00000502463.7	TSL:2	n.144-4173G>T		intron	N/A

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

African (AFR) AF: 0.339 AC: 14060 AN: 41436

American (AMR) AF: 0.411 AC: 6283 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1180 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1614 AN: 5170

South Asian (SAS) AF: 0.225 AC: 1079 AN: 4806

European-Finnish (FIN) AF: 0.295 AC: 3118 AN: 10562

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22582 AN: 67994

Other (OTH) AF: 0.353 AC: 746 AN: 2116

Alfa AF: 0.333 Hom.: 15120

Bravo AF: 0.347

Asia WGS AF: 0.278 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10096900; hg19: chr8-128708284;