rs4645943

Positions:

• chr8-127735225-C-T

Variant summary

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

The ENST00000672942.1(CASC11):​n.195-1266G>A 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 0.14 in 152,032 control chromosomes in the GnomAD database, including 2,596 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 0.14 (2596 hom., cov: 32)
• Consequence: CASC11 ENST00000672942.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC11	ENST00000672942.1	n.195-1266G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21281 AN: 151912 Hom.: 2587 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0577

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0431

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.140 AC: 21329 AN: 152032 Hom.: 2596 Cov.: 32 AF XY: 0.144 AC XY: 10702 AN XY: 74322

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0577

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0930

Gnomad4 NFE AF: 0.0431

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.0705 Hom.: 548

Bravo AF: 0.144

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4645943; hg19: chr8-128747471; COSMIC: COSV104583428;