rs552487543
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PM4_Supporting
The NM_001277115.2(DNAH11):c.13351_13353delAAG(p.Lys4451del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000192 in 1,613,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
DNAH11
NM_001277115.2 conservative_inframe_deletion
NM_001277115.2 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.29
Publications
1 publications found
Genes affected
DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]
CDCA7L (HGNC:30777): (cell division cycle associated 7 like) Acts upstream of or within positive regulation of cell population proliferation. Located in cytosol; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001277115.2. Strenght limited to Supporting due to length of the change: 1aa.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001277115.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DNAH11 | NM_001277115.2 | MANE Select | c.13351_13353delAAG | p.Lys4451del | conservative_inframe_deletion | Exon 82 of 82 | NP_001264044.1 | ||
| CDCA7L | NM_018719.5 | MANE Select | c.*1266_*1268delCTT | 3_prime_UTR | Exon 10 of 10 | NP_061189.2 | |||
| CDCA7L | NM_001127370.3 | c.*1266_*1268delCTT | 3_prime_UTR | Exon 11 of 11 | NP_001120842.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DNAH11 | ENST00000409508.8 | TSL:5 MANE Select | c.13351_13353delAAG | p.Lys4451del | conservative_inframe_deletion | Exon 82 of 82 | ENSP00000475939.1 | ||
| CDCA7L | ENST00000406877.8 | TSL:1 MANE Select | c.*1266_*1268delCTT | 3_prime_UTR | Exon 10 of 10 | ENSP00000383986.3 | |||
| DNAH11 | ENST00000479878.1 | TSL:3 | n.722_724delAAG | non_coding_transcript_exon | Exon 5 of 5 |
Frequencies
GnomAD3 genomes 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
152212
Hom.:
Cov.:
33
Gnomad AFR
AF:
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GnomAD2 exomes AF: 0.0000201 AC: 5AN: 248304 AF XY: 0.0000148 show subpopulations
GnomAD2 exomes
AF:
AC:
5
AN:
248304
AF XY:
Gnomad AFR exome
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Gnomad ASJ exome
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GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461064Hom.: 0 AF XY: 0.0000206 AC XY: 15AN XY: 726798 show subpopulations
GnomAD4 exome
AF:
AC:
27
AN:
1461064
Hom.:
AF XY:
AC XY:
15
AN XY:
726798
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33454
American (AMR)
AF:
AC:
3
AN:
44624
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26092
East Asian (EAS)
AF:
AC:
0
AN:
39694
South Asian (SAS)
AF:
AC:
0
AN:
86120
European-Finnish (FIN)
AF:
AC:
0
AN:
53392
Middle Eastern (MID)
AF:
AC:
0
AN:
5762
European-Non Finnish (NFE)
AF:
AC:
24
AN:
1111580
Other (OTH)
AF:
AC:
0
AN:
60346
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.466
Heterozygous variant carriers
0
2
4
7
9
11
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74360 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
152212
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
74360
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41454
American (AMR)
AF:
AC:
0
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
2
AN:
68048
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.513
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.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Primary ciliary dyskinesia (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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