ENST00000652081.2:n.145+50712A>G

Variant names:

• chr6-22403363-A-G
• rs10484722
• ENST00000652081.2:n.145+50712A>G

Variant summary

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

The ENST00000652081.2(CASC15):​n.145+50712A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,154 control chromosomes in the GnomAD database, including 1,806 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 0.11 (1806 hom., cov: 32)
• Consequence: CASC15 ENST00000652081.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374971	XR_001744024.2	n.482+2720A>G		intron_variant	Intron 3 of 4
LOC105374971	XR_001744025.1	n.402+2720A>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000652081.2	n.145+50712A>G		intron_variant	Intron 2 of 7
CASC15	ENST00000846434.1	n.346+50712A>G		intron_variant	Intron 2 of 5
CASC15	ENST00000846435.1	n.351+50712A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16671 AN: 152036 Hom.: 1800 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.110 AC: 16697 AN: 152154 Hom.: 1806 Cov.: 32 AF XY: 0.106 AC XY: 7886 AN XY: 74414

African (AFR) AF: 0.285 AC: 11817 AN: 41452

American (AMR) AF: 0.0572 AC: 874 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5188

South Asian (SAS) AF: 0.0544 AC: 262 AN: 4820

European-Finnish (FIN) AF: 0.0145 AC: 154 AN: 10624

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0451 AC: 3065 AN: 67988

Other (OTH) AF: 0.0960 AC: 203 AN: 2114

Alfa AF: 0.0642 Hom.: 1006

Bravo AF: 0.122

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.41
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs10484722; hg19: chr6-22403592;