6-22382678-T-C

Variant names:

• chr6-22382678-T-C
• rs719332
• ENST00000652081.2:n.145+30027T>C

Variant summary

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

The ENST00000652081.2(CASC15):​n.145+30027T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,116 control chromosomes in the GnomAD database, including 18,394 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 0.49 (18394 hom., cov: 33)
• Consequence: CASC15 ENST00000652081.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• 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]

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 (SAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374971	XR_001744024.2	n.368-17851T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000652081.2	n.145+30027T>C		intron_variant	Intron 2 of 7
CASC15	ENST00000846434.1	n.346+30027T>C		intron_variant	Intron 2 of 5
CASC15	ENST00000846435.1	n.351+30027T>C		intron_variant	Intron 2 of 2
CASC15	ENST00000846436.1	n.272-17908T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74487 AN: 151998 Hom.: 18362 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.490 AC: 74570 AN: 152116 Hom.: 18394 Cov.: 33 AF XY: 0.493 AC XY: 36668 AN XY: 74364

African (AFR) AF: 0.532 AC: 22087 AN: 41494

American (AMR) AF: 0.510 AC: 7791 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2707 AN: 5172

South Asian (SAS) AF: 0.616 AC: 2967 AN: 4820

European-Finnish (FIN) AF: 0.477 AC: 5049 AN: 10596

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30519 AN: 67988

Other (OTH) AF: 0.468 AC: 986 AN: 2108

Alfa AF: 0.469 Hom.: 52768

Bravo AF: 0.493

Asia WGS AF: 0.605 AC: 2104 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	0.017
DANN	Benign	0.30
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs719332; hg19: chr6-22382907;