rs9295536

Variant names:

• chr6-22131700-C-A
• rs9295536
• ENST00000444265.6:n.1061+20780C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-22131700-C-A
• chr6-22131700-C-G

Variant summary

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

The ENST00000444265.6(CASC15):​n.1061+20780C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,844 control chromosomes in the GnomAD database, including 27,752 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 0.58 (27752 hom., cov: 30)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 32 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444265.6. 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
	CASC15	NR_015410.2		n.1422+20780C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC15	ENST00000444265.6	TSL:1	n.1061+20780C>A		intron	N/A
	CASC15	ENST00000606851.5	TSL:2	n.1391+20780C>A		intron	N/A
	CASC15	ENST00000607048.5	TSL:2	n.1138+17663C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88156 AN: 151726 Hom.: 27713 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.581 AC: 88249 AN: 151844 Hom.: 27752 Cov.: 30 AF XY: 0.586 AC XY: 43506 AN XY: 74186

African (AFR) AF: 0.816 AC: 33800 AN: 41430

American (AMR) AF: 0.611 AC: 9318 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1437 AN: 3464

East Asian (EAS) AF: 0.733 AC: 3775 AN: 5148

South Asian (SAS) AF: 0.571 AC: 2742 AN: 4800

European-Finnish (FIN) AF: 0.561 AC: 5904 AN: 10518

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29486 AN: 67918

Other (OTH) AF: 0.537 AC: 1132 AN: 2108

Alfa AF: 0.480 Hom.: 82367

Bravo AF: 0.596

Asia WGS AF: 0.642 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.55
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9295536; hg19: chr6-22131929;