Variant 6-22117206-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000444265.6(CASC15):n.1061+6286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,172 control chromosomes in the GnomAD database, including 205 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 0.039 ( 205 hom., cov: 32)

Consequence

CASC15
ENST00000444265.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.390

Variant links:

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]

CASC15 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC15	NR_015410.2 link	n.1422+6286C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CASC15	ENST00000444265.6 link	n.1061+6286C>T	intron_variant	1
CASC15	ENST00000606851.5 link	n.1391+6286C>T	intron_variant	2
CASC15	ENST00000607048.5 link	n.1138+3169C>T	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0392

AC:

5960

AN:

152054

Hom.:

204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0567

Gnomad AMI

AF:

0.0493

Gnomad AMR

AF:

0.0260

Gnomad ASJ

AF:

0.00865

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.0213

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0237

Gnomad OTH

AF:

0.0268

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

GnomAD4 genome

AF:

0.0392

AC:

5965

AN:

152172

Hom.:

205

Cov.:

AF XY:

0.0406

AC XY:

3020

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0567

Gnomad4 AMR

AF:

0.0259

Gnomad4 ASJ

AF:

0.00865

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.0213

Gnomad4 NFE

AF:

0.0237

Gnomad4 OTH

AF:

0.0260

Alfa

AF:

0.0251

Hom.:

Bravo

AF:

0.0369

Asia WGS

AF:

0.104

AC:

361

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.23

DANN

Benign

0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over