rs560113507
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001256715.2(DNAAF3):c.1017C>T(p.His339His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
DNAAF3
NM_001256715.2 synonymous
NM_001256715.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.363
Publications
1 publications found
Genes affected
DNAAF3 (HGNC:30492): (dynein axonemal assembly factor 3) The protein encoded by this gene is required for the assembly of axonemal inner and outer dynein arms and plays a role in assembling dynein complexes for transport into cilia. Defects in this gene are a cause of primary ciliary dyskinesia type 2 (CILD2). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP7
Synonymous conserved (PhyloP=-0.363 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001256715.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DNAAF3 | NM_001256715.2 | MANE Select | c.1017C>T | p.His339His | synonymous | Exon 9 of 12 | NP_001243644.1 | ||
| DNAAF3 | NM_001256714.1 | c.1221C>T | p.His407His | synonymous | Exon 9 of 12 | NP_001243643.1 | |||
| DNAAF3 | NM_178837.4 | c.1158C>T | p.His386His | synonymous | Exon 9 of 12 | NP_849159.2 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DNAAF3 | ENST00000524407.7 | TSL:1 MANE Select | c.1017C>T | p.His339His | synonymous | Exon 9 of 12 | ENSP00000432046.3 | ||
| DNAAF3 | ENST00000455045.5 | TSL:1 | c.855C>T | p.His285His | synonymous | Exon 9 of 12 | ENSP00000394343.1 | ||
| DNAAF3 | ENST00000528412.5 | TSL:1 | n.*805C>T | non_coding_transcript_exon | Exon 9 of 12 | ENSP00000433826.2 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152116
Hom.:
Cov.:
32
Gnomad AFR
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000806 AC: 2AN: 248278 AF XY: 0.0000148 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
248278
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461616Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727114 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1461616
Hom.:
Cov.:
33
AF XY:
AC XY:
3
AN XY:
727114
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33478
American (AMR)
AF:
AC:
0
AN:
44716
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26128
East Asian (EAS)
AF:
AC:
0
AN:
39692
South Asian (SAS)
AF:
AC:
2
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53246
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111944
Other (OTH)
AF:
AC:
0
AN:
60388
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
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2
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Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74442 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
152234
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74442
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
41534
American (AMR)
AF:
AC:
0
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5158
South Asian (SAS)
AF:
AC:
1
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10602
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68012
Other (OTH)
AF:
AC:
0
AN:
2114
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 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: 0.375
Heterozygous variant carriers
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0
1
1
2
2
0.00
0.20
0.40
0.60
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0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
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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