rs10094872

Variant names:

• chr8-127707639-A-T
• rs10094872
• ENST00000502463.7:n.144-15773T>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000502463.7(CASC11):​n.144-15773T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,072 control chromosomes in the GnomAD database, including 8,655 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 0.33 (8655 hom., cov: 32)
• Consequence: CASC11 ENST00000502463.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC11	NR_117102.1	n.366-4396T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC11	ENST00000502463.7	n.144-15773T>A		intron_variant	Intron 1 of 2	2
CASC11	ENST00000519071.6	n.355-4396T>A		intron_variant	Intron 2 of 3	3
CASC11	ENST00000672637.1	n.272-4396T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49968 AN: 151954 Hom.: 8651 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.329 AC: 49985 AN: 152072 Hom.: 8655 Cov.: 32 AF XY: 0.331 AC XY: 24571 AN XY: 74344

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.322

Alfa AF: 0.366 Hom.: 1342

Bravo AF: 0.307

Asia WGS AF: 0.300 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	19
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10094872; hg19: chr8-128719884;