rs9356811

Positions:

• chr6-22308068-G-A
• chr6-22308068-G-C
• chr6-22308068-G-T

Variant summary

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

The ENST00000561912.3(CASC15):​n.570-8759G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.32 (7408 hom., cov: 19)
• Consequence: CASC15 ENST00000561912.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 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.570-8759G>A		intron_variant, non_coding_transcript_variant		5
CASC15	ENST00000651569.1	n.506-8759G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.320 AC: 41056 AN: 128282 Hom.: 7413 Cov.: 19

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.320 AC: 41049 AN: 128308 Hom.: 7408 Cov.: 19 AF XY: 0.323 AC XY: 19605 AN XY: 60642

Gnomad4 AFR AF: 0.0916

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.345

Alfa AF: 0.156 Hom.: 330

Bravo AF: 0.283

Asia WGS AF: 0.268 AC: 928 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9356811; hg19: chr6-22308297;