GeneBe

ENST00000561912.3:n.800-475A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000561912.3(CASC15):​n.800-475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,106 control chromosomes in the GnomAD database, including 7,834 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 0.29 ( 7834 hom., cov: 33)

Consequence

CASC15
ENST00000561912.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

Publications

6 publications found
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]

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ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC15ENST00000561912.3 linkn.800-475A>G intron_variant Intron 7 of 10 5

Frequencies

GnomAD3 genomes
AF:
0.290
AC:
44077
AN:
151988
Hom.:
7834
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0774
Gnomad AMI
AF:
0.384
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.346
Gnomad EAS
AF:
0.373
Gnomad SAS
AF:
0.251
Gnomad FIN
AF:
0.415
Gnomad MID
AF:
0.334
Gnomad NFE
AF:
0.387
Gnomad OTH
AF:
0.295
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.290
AC:
44090
AN:
152106
Hom.:
7834
Cov.:
33
AF XY:
0.293
AC XY:
21773
AN XY:
74314
show subpopulations
African (AFR)
AF:
0.0772
AC:
3205
AN:
41540
American (AMR)
AF:
0.311
AC:
4755
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.346
AC:
1203
AN:
3472
East Asian (EAS)
AF:
0.374
AC:
1934
AN:
5174
South Asian (SAS)
AF:
0.254
AC:
1225
AN:
4820
European-Finnish (FIN)
AF:
0.415
AC:
4378
AN:
10552
Middle Eastern (MID)
AF:
0.325
AC:
95
AN:
292
European-Non Finnish (NFE)
AF:
0.387
AC:
26319
AN:
67962
Other (OTH)
AF:
0.297
AC:
626
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1494
2989
4483
5978
7472
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
444
888
1332
1776
2220
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.352
Hom.:
31561
Bravo
AF:
0.274
Asia WGS
AF:
0.270
AC:
939
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.13
DANN
Benign
0.73
PhyloP100
-1.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs1935007; hg19: chr6-22343301; API