GeneBe

ENST00000502056.1:n.1041+11791A>G

Variant names:

Variant summary

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

The ENST00000502056.1(CASC8):​n.1041+11791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 151,700 control chromosomes in the GnomAD database, including 48,063 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 0.79 ( 48063 hom., cov: 33)

Consequence

CASC8
ENST00000502056.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Publications

5 publications found
Variant links:
Genes affected
CASC8 (HGNC:45129): (cancer susceptibility 8)

Genome browser will be placed here

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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CASC8NR_024393.1 linkn.1041+11791A>G intron_variant Intron 4 of 4
CASC8NR_117100.1 linkn.1041+11791A>G intron_variant Intron 4 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC8ENST00000502056.1 linkn.1041+11791A>G intron_variant Intron 4 of 4 1
CASC8ENST00000502082.5 linkn.1041+11791A>G intron_variant Intron 4 of 5 1

Frequencies

GnomAD3 genomes
AF:
0.791
AC:
119828
AN:
151582
Hom.:
48065
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.643
Gnomad AMI
AF:
0.903
Gnomad AMR
AF:
0.829
Gnomad ASJ
AF:
0.923
Gnomad EAS
AF:
0.738
Gnomad SAS
AF:
0.826
Gnomad FIN
AF:
0.774
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.865
Gnomad OTH
AF:
0.833
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.790
AC:
119860
AN:
151700
Hom.:
48063
Cov.:
33
AF XY:
0.787
AC XY:
58375
AN XY:
74128
show subpopulations
African (AFR)
AF:
0.642
AC:
26536
AN:
41332
American (AMR)
AF:
0.828
AC:
12647
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.923
AC:
3204
AN:
3470
East Asian (EAS)
AF:
0.738
AC:
3796
AN:
5146
South Asian (SAS)
AF:
0.826
AC:
3985
AN:
4822
European-Finnish (FIN)
AF:
0.774
AC:
8127
AN:
10498
Middle Eastern (MID)
AF:
0.946
AC:
278
AN:
294
European-Non Finnish (NFE)
AF:
0.866
AC:
58722
AN:
67846
Other (OTH)
AF:
0.827
AC:
1747
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1250
2500
3750
5000
6250
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
864
1728
2592
3456
4320
<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:
0.821
Hom.:
13840
Bravo
AF:
0.785
Asia WGS
AF:
0.722
AC:
2510
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.2
DANN
Benign
0.64
PhyloP100
-0.17

Splicing

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

Publications

Other links and lift over

dbSNP: rs3999775; hg19: chr8-128479537; API