rs9358531

Variant names:

• chr6-22309401-T-G
• rs9358531
• ENST00000561912.3:n.570-7426T>G

Variant summary

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

The ENST00000561912.3(CASC15):​n.570-7426T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,002 control chromosomes in the GnomAD database, including 9,517 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 0.33 (9517 hom., cov: 31)
• Consequence: CASC15 ENST00000561912.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000561912.3	n.570-7426T>G		intron_variant	Intron 4 of 10	5
CASC15	ENST00000651569.1	n.506-7426T>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49848 AN: 151884 Hom.: 9521 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.328 AC: 49853 AN: 152002 Hom.: 9517 Cov.: 31 AF XY: 0.328 AC XY: 24371 AN XY: 74288

Gnomad4 AFR AF: 0.136 AC: 0.135519 AN: 0.135519

Gnomad4 AMR AF: 0.339 AC: 0.338507 AN: 0.338507

Gnomad4 ASJ AF: 0.424 AC: 0.423832 AN: 0.423832

Gnomad4 EAS AF: 0.383 AC: 0.383165 AN: 0.383165

Gnomad4 SAS AF: 0.273 AC: 0.272973 AN: 0.272973

Gnomad4 FIN AF: 0.393 AC: 0.393236 AN: 0.393236

Gnomad4 NFE AF: 0.426 AC: 0.425959 AN: 0.425959

Gnomad4 OTH AF: 0.369 AC: 0.368596 AN: 0.368596

Alfa AF: 0.364 Hom.: 2398

Bravo AF: 0.317

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9358531; hg19: chr6-22309630;