3-180631612-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_181426.2(CCDC39):c.1875-20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000813 in 1,589,300 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0043 ( 8 hom., cov: 32)
Exomes 𝑓: 0.00044 ( 5 hom. )
Consequence
CCDC39
NM_181426.2 intron
NM_181426.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.756
Publications
0 publications found
Genes affected
CCDC39 (HGNC:25244): (coiled-coil domain 39 molecular ruler complex subunit) The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]
CCDC39 Gene-Disease associations (from GenCC):
- primary ciliary dyskinesia 14Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
- primary ciliary dyskinesiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 3-180631612-C-T is Benign according to our data. Variant chr3-180631612-C-T is described in ClinVar as [Benign]. Clinvar id is 262965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00434 (661/152228) while in subpopulation AFR AF = 0.015 (623/41540). AF 95% confidence interval is 0.014. There are 8 homozygotes in GnomAd4. There are 295 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 8 AD,AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00435 AC: 661AN: 152110Hom.: 8 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
661
AN:
152110
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:
GnomAD2 exomes AF: 0.00113 AC: 246AN: 218262 AF XY: 0.000801 show subpopulations
GnomAD2 exomes
AF:
AC:
246
AN:
218262
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000439 AC: 631AN: 1437072Hom.: 5 Cov.: 28 AF XY: 0.000391 AC XY: 279AN XY: 714384 show subpopulations
GnomAD4 exome
AF:
AC:
631
AN:
1437072
Hom.:
Cov.:
28
AF XY:
AC XY:
279
AN XY:
714384
show subpopulations
African (AFR)
AF:
AC:
544
AN:
32822
American (AMR)
AF:
AC:
31
AN:
41522
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25866
East Asian (EAS)
AF:
AC:
0
AN:
39468
South Asian (SAS)
AF:
AC:
1
AN:
83510
European-Finnish (FIN)
AF:
AC:
0
AN:
45142
Middle Eastern (MID)
AF:
AC:
0
AN:
5742
European-Non Finnish (NFE)
AF:
AC:
8
AN:
1103260
Other (OTH)
AF:
AC:
47
AN:
59740
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.477
Heterozygous variant carriers
0
28
56
83
111
139
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.00434 AC: 661AN: 152228Hom.: 8 Cov.: 32 AF XY: 0.00396 AC XY: 295AN XY: 74430 show subpopulations
GnomAD4 genome
AF:
AC:
661
AN:
152228
Hom.:
Cov.:
32
AF XY:
AC XY:
295
AN XY:
74430
show subpopulations
African (AFR)
AF:
AC:
623
AN:
41540
American (AMR)
AF:
AC:
25
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5188
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10590
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
4
AN:
68012
Other (OTH)
AF:
AC:
9
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
31
62
94
125
156
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<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:
2
AN:
3476
ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Primary ciliary dyskinesia Benign:1
Jan 23, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Primary ciliary dyskinesia 14 Benign:1
May 20, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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