rs11759745

chr6-22114901-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_015410.2(CASC15):n.1422+3981A>C 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 0.366 in 152,006 control chromosomes in the GnomAD database, including 10,596 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 0.37 (10596 hom., cov: 32)
• Consequence: CASC15 NR_015410.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

CASC15 (HGNC:28245): (cancer susceptibility 15) This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC15	NR_015410.2	n.1422+3981A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC15	ENST00000688254.1	n.1151+58211A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55547 AN: 151888 Hom.: 10587 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.366 AC: 55588 AN: 152006 Hom.: 10596 Cov.: 32 AF XY: 0.365 AC XY: 27111 AN XY: 74298

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.346

Alfa AF: 0.336 Hom.: 9775

Bravo AF: 0.361

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
Cadd	Benign	14
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11759745; hg19: chr6-22115130;