rs7840975

Variant names:

• chr8-127692916-C-T
• rs7840975
• ENST00000502463.7:n.144-1050G>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC11	ENST00000502463.7	n.144-1050G>A		intron_variant	Intron 1 of 2	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;