rs6939340

Variant names:

• chr6-22139775-A-G
• rs6939340
• ENST00000444265.6:n.1061+28855A>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+28855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,118 control chromosomes in the GnomAD database, including 30,806 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 0.62 (30806 hom., cov: 32)
• Consequence: CASC15 ENST00000444265.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 59 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]

NBAT1 (HGNC:49075): (neuroblastoma associated transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CASC15	NR_015410.2	n.1422+28855A>G		intron_variant	Intron 9 of 11
NBAT1	NR_034143.1	n.228-3106T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.1061+28855A>G		intron_variant	Intron 7 of 10	1
NBAT1	ENST00000566912.2	n.228-3106T>C		intron_variant	Intron 2 of 2	2
CASC15	ENST00000606851.5	n.1391+28855A>G		intron_variant	Intron 9 of 11	2

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93666 AN: 152000 Hom.: 30753 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.616 AC: 93773 AN: 152118 Hom.: 30806 Cov.: 32 AF XY: 0.621 AC XY: 46154 AN XY: 74360

African (AFR) AF: 0.844 AC: 35048 AN: 41522

American (AMR) AF: 0.630 AC: 9633 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3447 AN: 5176

South Asian (SAS) AF: 0.631 AC: 3038 AN: 4816

European-Finnish (FIN) AF: 0.609 AC: 6427 AN: 10562

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32756 AN: 67972

Other (OTH) AF: 0.572 AC: 1204 AN: 2104

Alfa AF: 0.516 Hom.: 95098

Bravo AF: 0.627

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.33
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs6939340; hg19: chr6-22140004;