rs7840975

Positions:

• chr8-127692916-C-T

Variant summary

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

The ENST00000502463.7(CASC11):​n.144-1050G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,146 control chromosomes in the GnomAD database, including 2,410 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 0.15 (2410 hom., cov: 33)
• Consequence: CASC11 ENST00000502463.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC11	ENST00000502463.7	n.144-1050G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22133 AN: 152028 Hom.: 2399 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.146 AC: 22182 AN: 152146 Hom.: 2410 Cov.: 33 AF XY: 0.148 AC XY: 11009 AN XY: 74394

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.0768

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0675

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0810 Hom.: 1350

Bravo AF: 0.146

Asia WGS AF: 0.218 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.021
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7840975; hg19: chr8-128705161;