rs1341239

chr6-22303975-A-C

Variant summary

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

The ENST00000561912.3(CASC15):n.570-12852A>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 0.656 in 151,918 control chromosomes in the GnomAD database, including 32,950 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 0.66 (32950 hom., cov: 31)
• Consequence: CASC15 ENST00000561912.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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
CASC15	ENST00000561912.3	n.570-12852A>C		intron_variant, non_coding_transcript_variant		5
CASC15	ENST00000651569.1	n.506-12852A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99614 AN: 151802 Hom.: 32907 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.656 AC: 99711 AN: 151918 Hom.: 32950 Cov.: 31 AF XY: 0.664 AC XY: 49265 AN XY: 74240

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.668

Alfa AF: 0.634 Hom.: 48406

Bravo AF: 0.664

Asia WGS AF: 0.801 AC: 2782 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.73
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341239; hg19: chr6-22304204;