rs12199382

Variant names:

• chr6-22326901-G-A
• rs12199382
• ENST00000561912.3:n.705+9103G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-22326901-G-A
• chr6-22326901-G-T

Variant summary

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

The ENST00000561912.3(CASC15):​n.705+9103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,958 control chromosomes in the GnomAD database, including 8,655 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 0.30 (8655 hom., cov: 33)
• Consequence: CASC15 ENST00000561912.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561912.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC15	ENST00000561912.3	TSL:5	n.705+9103G>A		intron	N/A
	CASC15	ENST00000651569.1		n.641+9103G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46264 AN: 151840 Hom.: 8653 Cov.: 33

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.305 AC: 46282 AN: 151958 Hom.: 8655 Cov.: 33 AF XY: 0.309 AC XY: 22913 AN XY: 74266

African (AFR) AF: 0.0819 AC: 3397 AN: 41492

American (AMR) AF: 0.323 AC: 4900 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1233 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1994 AN: 5176

South Asian (SAS) AF: 0.264 AC: 1275 AN: 4824

European-Finnish (FIN) AF: 0.452 AC: 4770 AN: 10546

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27575 AN: 67962

Other (OTH) AF: 0.328 AC: 693 AN: 2116

Alfa AF: 0.288 Hom.: 2511

Bravo AF: 0.285

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.60
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12199382; hg19: chr6-22327130;