rs754233819
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_ModerateBP6_ModerateBP7
The NM_012144.4(DNAI1):c.1002C>A(p.Ser334Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,680 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S334S) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DNAI1
NM_012144.4 synonymous
NM_012144.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.48
Publications
0 publications found
Genes affected
DNAI1 (HGNC:2954): (dynein axonemal intermediate chain 1) This gene encodes a member of the dynein intermediate chain family. The encoded protein is part of the dynein complex in respiratory cilia. The inner- and outer-arm dyneins, which bridge between the doublet microtubules in axonemes, are the force-generating proteins responsible for the sliding movement in axonemes. The intermediate and light chains, thought to form the base of the dynein arm, help mediate attachment and may also participate in regulating dynein activity. Mutations in this gene result in abnormal ciliary ultrastructure and function associated with primary ciliary dyskinesia and Kartagener syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
DNAI1 Gene-Disease associations (from GenCC):
- primary ciliary dyskinesia 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, PanelApp Australia
- 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 -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 9-34500822-C-A is Benign according to our data. Variant chr9-34500822-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1123216.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.48 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| DNAI1 | NM_012144.4 | c.1002C>A | p.Ser334Ser | synonymous_variant | Exon 11 of 20 | ENST00000242317.9 | NP_036276.1 | |
| DNAI1 | NM_001281428.2 | c.1014C>A | p.Ser338Ser | synonymous_variant | Exon 11 of 20 | NP_001268357.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DNAI1 | ENST00000242317.9 | c.1002C>A | p.Ser334Ser | synonymous_variant | Exon 11 of 20 | 1 | NM_012144.4 | ENSP00000242317.4 | ||
| DNAI1 | ENST00000614641.4 | c.1014C>A | p.Ser338Ser | synonymous_variant | Exon 11 of 20 | 5 | ENSP00000480538.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 152206Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
152206
Hom.:
Cov.:
32
Gnomad AFR
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461680Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727170 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1461680
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
727170
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33476
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39696
South Asian (SAS)
AF:
AC:
0
AN:
86246
European-Finnish (FIN)
AF:
AC:
0
AN:
53418
Middle Eastern (MID)
AF:
AC:
0
AN:
5748
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111850
Other (OTH)
AF:
AC:
0
AN:
60386
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
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1
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0.95
Allele balance
GnomAD4 genome 0.00 AC: 0AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
152206
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74356
African (AFR)
AF:
AC:
0
AN:
41442
American (AMR)
AF:
AC:
0
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5196
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10622
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68048
Other (OTH)
AF:
AC:
0
AN:
2092
Alfa
AF:
Hom.:
EpiCase
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EpiControl
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Jun 21, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely 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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