rs11990827

chr8-127704634-A-Cchr8-127704634-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_117102.1(CASC11):n.366-1391T>G variant causes a intron, non coding transcript 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 NR_117102.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CASC11	NR_117102.1	n.366-1391T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC11	ENST00000502463.7	n.144-12768T>G		intron_variant, non_coding_transcript_variant		2
CASC11	ENST00000519071.6	n.355-1391T>G		intron_variant, non_coding_transcript_variant		3
CASC11	ENST00000672637.1	n.272-1391T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0221

Gnomad4 FIN AF: 0.00980

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0635

Alfa AF: 0.0418 Hom.: 137

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11990827; hg19: chr8-128716879;