rs10839963

Positions:

• chr11-8015348-T-A
• chr11-8015348-T-C
• chr11-8015348-T-G

Variant summary

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

The NR_125366.1(CASC23):​n.435+727A>T 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 0.431 in 151,946 control chromosomes in the GnomAD database, including 15,034 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 0.43 (15034 hom., cov: 32)
• Consequence: CASC23 NR_125366.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

Genes affected

CASC23 (HGNC:50865): (cancer susceptibility 23)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC23	NR_125366.1	n.435+727A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC23	ENST00000534076.2	n.446+727A>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65450 AN: 151828 Hom.: 14994 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.431 AC: 65543 AN: 151946 Hom.: 15034 Cov.: 32 AF XY: 0.434 AC XY: 32243 AN XY: 74242

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.425

Alfa AF: 0.395 Hom.: 1714

Bravo AF: 0.452

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10839963; hg19: chr11-8036895;