3-180647255-TAA-TAAAA
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_181426.2(CCDC39):c.1363-14_1363-13dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00057 in 1,284,600 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0000069 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00064 ( 0 hom. )
Consequence
CCDC39
NM_181426.2 intron
NM_181426.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.273
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: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae), ClinGen
- primary ciliary dyskinesiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP6
Variant 3-180647255-T-TAA is Benign according to our data. Variant chr3-180647255-T-TAA is described in ClinVar as Benign. ClinVar VariationId is 2896815.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_181426.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CCDC39 | NM_181426.2 | MANE Select | c.1363-14_1363-13dupTT | intron | N/A | NP_852091.1 | Q9UFE4-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CCDC39 | ENST00000476379.6 | TSL:2 MANE Select | c.1363-13_1363-12insTT | intron | N/A | ENSP00000417960.2 | Q9UFE4-1 | ||
| CCDC39 | ENST00000936067.1 | c.1270-13_1270-12insTT | intron | N/A | ENSP00000606126.1 | ||||
| CCDC39 | ENST00000651046.1 | c.1171-13_1171-12insTT | intron | N/A | ENSP00000499175.1 | A0A494C1Q3 |
Frequencies
GnomAD3 genomes 0.00000692 AC: 1AN: 144554Hom.: 0 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
144554
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000794 AC: 60AN: 75564 AF XY: 0.000876 show subpopulations
GnomAD2 exomes
AF:
AC:
60
AN:
75564
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000641 AC: 731AN: 1140046Hom.: 0 Cov.: 24 AF XY: 0.000691 AC XY: 388AN XY: 561670 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
731
AN:
1140046
Hom.:
Cov.:
24
AF XY:
AC XY:
388
AN XY:
561670
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
3
AN:
23862
American (AMR)
AF:
AC:
17
AN:
20740
Ashkenazi Jewish (ASJ)
AF:
AC:
13
AN:
18788
East Asian (EAS)
AF:
AC:
1
AN:
28234
South Asian (SAS)
AF:
AC:
35
AN:
59318
European-Finnish (FIN)
AF:
AC:
39
AN:
40240
Middle Eastern (MID)
AF:
AC:
4
AN:
4618
European-Non Finnish (NFE)
AF:
AC:
589
AN:
897842
Other (OTH)
AF:
AC:
30
AN:
46404
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.257
Heterozygous variant carriers
0
100
199
299
398
498
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
24
48
72
96
120
<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 0.00000692 AC: 1AN: 144554Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 70092 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
144554
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
70092
show subpopulations
African (AFR)
AF:
AC:
0
AN:
39242
American (AMR)
AF:
AC:
0
AN:
14464
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3362
East Asian (EAS)
AF:
AC:
0
AN:
5016
South Asian (SAS)
AF:
AC:
0
AN:
4602
European-Finnish (FIN)
AF:
AC:
0
AN:
8966
Middle Eastern (MID)
AF:
AC:
0
AN:
302
European-Non Finnish (NFE)
AF:
AC:
1
AN:
65750
Other (OTH)
AF:
AC:
0
AN:
1962
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Primary ciliary dyskinesia (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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