rs10094872

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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
	CASC11	NR_117102.1		n.366-4396T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	ENST00000502463.7	TSL:2	n.144-15773T>A		intron	N/A
	CASC11	ENST00000519071.6	TSL:3	n.355-4396T>A		intron	N/A
	CASC11	ENST00000672637.1		n.272-4396T>A		intron	N/A

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

African (AFR) AF: 0.279 AC: 11570 AN: 41480

American (AMR) AF: 0.225 AC: 3436 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.191 AC: 993 AN: 5190

South Asian (SAS) AF: 0.362 AC: 1748 AN: 4824

European-Finnish (FIN) AF: 0.461 AC: 4864 AN: 10558

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25153 AN: 67972

Other (OTH) AF: 0.322 AC: 681 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	19
DANN	Benign	0.81
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs10094872; hg19: chr8-128719884;