chr18-33263452-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001105528.4(CCDC178):c.1409+3464G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,002 control chromosomes in the GnomAD database, including 1,317 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 0.11 ( 1317 hom., cov: 32)
Consequence
CCDC178
NM_001105528.4 intron
NM_001105528.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.187
Publications
5 publications found
Genes affected
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.110 AC: 16654AN: 151884Hom.: 1317 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
16654
AN:
151884
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.110 AC: 16656AN: 152002Hom.: 1317 Cov.: 32 AF XY: 0.111 AC XY: 8225AN XY: 74256 show subpopulations
GnomAD4 genome
AF:
AC:
16656
AN:
152002
Hom.:
Cov.:
32
AF XY:
AC XY:
8225
AN XY:
74256
show subpopulations
African (AFR)
AF:
AC:
1170
AN:
41500
American (AMR)
AF:
AC:
2025
AN:
15252
Ashkenazi Jewish (ASJ)
AF:
AC:
424
AN:
3472
East Asian (EAS)
AF:
AC:
1725
AN:
5150
South Asian (SAS)
AF:
AC:
1042
AN:
4806
European-Finnish (FIN)
AF:
AC:
614
AN:
10548
Middle Eastern (MID)
AF:
AC:
59
AN:
294
European-Non Finnish (NFE)
AF:
AC:
9318
AN:
67956
Other (OTH)
AF:
AC:
266
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
722
1444
2167
2889
3611
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
204
408
612
816
1020
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
784
AN:
3470
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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