rs6908475

Variant names:

• chr6-22572569-T-C
• rs6908475
• ENST00000652081.2:n.146-1550T>C

Variant summary

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

The ENST00000652081.2(CASC15):​n.146-1550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,050 control chromosomes in the GnomAD database, including 7,127 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 (7127 hom., cov: 32)
• Consequence: CASC15 ENST00000652081.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 3 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]

LOC105374971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652081.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC15	ENST00000652081.2		n.146-1550T>C		intron	N/A
	CASC15	ENST00000846434.1		n.433-1550T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45401 AN: 151934 Hom.: 7127 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.299 AC: 45410 AN: 152050 Hom.: 7127 Cov.: 32 AF XY: 0.293 AC XY: 21752 AN XY: 74312

African (AFR) AF: 0.234 AC: 9713 AN: 41500

American (AMR) AF: 0.326 AC: 4978 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3470

East Asian (EAS) AF: 0.179 AC: 926 AN: 5176

South Asian (SAS) AF: 0.241 AC: 1163 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2790 AN: 10544

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23482 AN: 67964

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.321 Hom.: 2057

Bravo AF: 0.302

Asia WGS AF: 0.253 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.26
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs6908475; hg19: chr6-22572798;