GeneBe

8-127482236-C-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.-97G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,228 control chromosomes in the GnomAD database, including 60,819 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 0.89 ( 60800 hom., cov: 30)
Exomes 𝑓: 0.90 ( 19 hom. )

Consequence

CASC8
ENST00000502056.1 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

Publications

11 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=-0.97).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CASC8NR_024393.1 linkn.-97G>C upstream_gene_variant
CASC8NR_117100.1 linkn.-97G>C upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CASC8ENST00000502056.1 linkn.-97G>C upstream_gene_variant 1
CASC8ENST00000502082.5 linkn.-97G>C upstream_gene_variant 1

Frequencies

GnomAD3 genomes
AF:
0.893
AC:
135836
AN:
152062
Hom.:
60751
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.893
Gnomad AMI
AF:
0.904
Gnomad AMR
AF:
0.924
Gnomad ASJ
AF:
0.940
Gnomad EAS
AF:
0.840
Gnomad SAS
AF:
0.872
Gnomad FIN
AF:
0.825
Gnomad MID
AF:
0.959
Gnomad NFE
AF:
0.900
Gnomad OTH
AF:
0.905
GnomAD4 exome
AF:
0.896
AC:
43
AN:
48
Hom.:
19
AF XY:
0.917
AC XY:
33
AN XY:
36
show subpopulations
African (AFR)
AF:
1.00
AC:
2
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AF:
1.00
AC:
2
AN:
2
East Asian (EAS)
AF:
1.00
AC:
2
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
1.00
AC:
2
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.861
AC:
31
AN:
36
Other (OTH)
AF:
1.00
AC:
4
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.535
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.893
AC:
135941
AN:
152180
Hom.:
60800
Cov.:
30
AF XY:
0.890
AC XY:
66252
AN XY:
74418
show subpopulations
African (AFR)
AF:
0.893
AC:
37061
AN:
41496
American (AMR)
AF:
0.924
AC:
14119
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.940
AC:
3265
AN:
3472
East Asian (EAS)
AF:
0.840
AC:
4341
AN:
5170
South Asian (SAS)
AF:
0.873
AC:
4215
AN:
4830
European-Finnish (FIN)
AF:
0.825
AC:
8740
AN:
10600
Middle Eastern (MID)
AF:
0.969
AC:
285
AN:
294
European-Non Finnish (NFE)
AF:
0.900
AC:
61197
AN:
68014
Other (OTH)
AF:
0.900
AC:
1894
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
726
1453
2179
2906
3632
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
902
1804
2706
3608
4510
<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:
0.835
Hom.:
1805
Bravo
AF:
0.898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.11
DANN
Benign
0.38
PhyloP100
-1.2
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs9643226; hg19: chr8-128494481; API