rs16902364

Variant names:

• chr8-127733020-A-C
• rs16902364
• ENST00000502463.7:n.143+805T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502463.7(CASC11):​n.143+805T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,038 control chromosomes in the GnomAD database, including 2,451 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 0.13 (2451 hom., cov: 32)
• Consequence: CASC11 ENST00000502463.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	NR_117101.1		n.143+805T>G		intron	N/A
	CASC11	NR_117102.1		n.143+805T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC11	ENST00000502463.7	TSL:2	n.143+805T>G		intron	N/A
	CASC11	ENST00000518376.2	TSL:3	n.141+805T>G		intron	N/A
	CASC11	ENST00000519071.6	TSL:3	n.132+805T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20004 AN: 151920 Hom.: 2438 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.132 AC: 20061 AN: 152038 Hom.: 2451 Cov.: 32 AF XY: 0.135 AC XY: 10051 AN XY: 74354

African (AFR) AF: 0.312 AC: 12942 AN: 41418

American (AMR) AF: 0.107 AC: 1639 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1085 AN: 5174

South Asian (SAS) AF: 0.153 AC: 736 AN: 4814

European-Finnish (FIN) AF: 0.0925 AC: 981 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2328 AN: 67974

Other (OTH) AF: 0.0873 AC: 184 AN: 2108

Alfa AF: 0.0647 Hom.: 2862

Bravo AF: 0.135

Asia WGS AF: 0.161 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs16902364; hg19: chr8-128745266; COSMIC: COSV104583426;