rs377278570
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PM2
The NM_012472.6(DNAAF11):c.2T>C(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,416,356 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
DNAAF11
NM_012472.6 start_lost
NM_012472.6 start_lost
Scores
4
9
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.35
Publications
0 publications found
Genes affected
DNAAF11 (HGNC:16725): (dynein axonemal assembly factor 11) The protein encoded by this gene contains several leucine-rich repeat domains and appears to be involved in the motility of cilia. Defects in this gene are a cause of primary ciliary dyskinesia-19 (CILD19). Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 11 and 22. [provided by RefSeq, Apr 2016]
DNAAF11 Gene-Disease associations (from GenCC):
- primary ciliary dyskinesia 19Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics, ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 10 ACMG points.
PVS1
Start lost variant, next in-frame start position is after 13 pathogenic variants. Next in-frame start position is after 121 codons. Genomic position: 132638003. Lost 0.258 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1416356Hom.: 0 Cov.: 30 AF XY: 0.00000284 AC XY: 2AN XY: 703728 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1416356
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
703728
show subpopulations
African (AFR)
AF:
AC:
1
AN:
31146
American (AMR)
AF:
AC:
0
AN:
40298
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25124
East Asian (EAS)
AF:
AC:
0
AN:
35458
South Asian (SAS)
AF:
AC:
1
AN:
81616
European-Finnish (FIN)
AF:
AC:
0
AN:
52722
Middle Eastern (MID)
AF:
AC:
0
AN:
5592
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1086156
Other (OTH)
AF:
AC:
0
AN:
58244
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.400
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;.;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Benign
T
PhyloP100
PROVEAN
Uncertain
.;D;D;D
REVEL
Uncertain
Sift
Uncertain
.;D;D;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
D;D;.;.
Vest4
MutPred
Loss of stability (P = 0.0412);Loss of stability (P = 0.0412);Loss of stability (P = 0.0412);Loss of stability (P = 0.0412);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.