rs9295552

Variant names:

• chr6-22540536-C-T
• rs9295552
• ENST00000652081.2:n.146-33583C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652081.2(CASC15):​n.146-33583C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,938 control chromosomes in the GnomAD database, including 17,278 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 0.47 (17278 hom., cov: 33)
• Consequence: CASC15 ENST00000652081.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 2 publications found

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]

LOC105374971 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652081.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC15	ENST00000652081.2		n.146-33583C>T		intron	N/A
	CASC15	ENST00000846434.1		n.432+22766C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71386 AN: 151820 Hom.: 17261 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.470 AC: 71447 AN: 151938 Hom.: 17278 Cov.: 33 AF XY: 0.462 AC XY: 34328 AN XY: 74246

African (AFR) AF: 0.542 AC: 22443 AN: 41436

American (AMR) AF: 0.351 AC: 5359 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3466

East Asian (EAS) AF: 0.154 AC: 799 AN: 5174

South Asian (SAS) AF: 0.326 AC: 1572 AN: 4826

European-Finnish (FIN) AF: 0.484 AC: 5109 AN: 10548

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33201 AN: 67910

Other (OTH) AF: 0.454 AC: 959 AN: 2112

Alfa AF: 0.477 Hom.: 21512

Bravo AF: 0.464

Asia WGS AF: 0.252 AC: 873 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.9
DANN	Benign	0.56
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs9295552; hg19: chr6-22540765;