rs11990827

Variant names:

• chr8-127704634-A-C
• rs11990827
• ENST00000502463.7:n.144-12768T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-127704634-A-C
• chr8-127704634-A-T

Variant summary

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

The ENST00000502463.7(CASC11):​n.144-12768T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,230 control chromosomes in the GnomAD database, including 1,423 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 0.082 (1423 hom., cov: 32)
• Consequence: CASC11 ENST00000502463.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC11	NR_117102.1	n.366-1391T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC11	ENST00000502463.7	n.144-12768T>G		intron_variant	Intron 1 of 2	2
CASC11	ENST00000519071.6	n.355-1391T>G		intron_variant	Intron 2 of 3	3
CASC11	ENST00000672637.1	n.272-1391T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12512 AN: 152112 Hom.: 1416 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0227

Gnomad FIN AF: 0.00980

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0824 AC: 12547 AN: 152230 Hom.: 1423 Cov.: 32 AF XY: 0.0801 AC XY: 5966 AN XY: 74438

African (AFR) AF: 0.256 AC: 10633 AN: 41498

American (AMR) AF: 0.0352 AC: 539 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.0221 AC: 107 AN: 4832

European-Finnish (FIN) AF: 0.00980 AC: 104 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0134 AC: 911 AN: 68022

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0502 Hom.: 174

Bravo AF: 0.0925

Asia WGS AF: 0.0350 AC: 123 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		0.056
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11990827; hg19: chr8-128716879;