rs9297853
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_012472.6(DNAAF11):āc.1397T>Cā(p.Ile466Thr) variant causes a missense change. The variant allele was found at a frequency of 0.1 in 1,611,468 control chromosomes in the GnomAD database, including 10,570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.15 ( 2573 hom., cov: 32)
Exomes š: 0.095 ( 7997 hom. )
Consequence
DNAAF11
NM_012472.6 missense
NM_012472.6 missense
Scores
8
5
Clinical Significance
Conservation
PhyloP100: 5.93
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0019569993).
BP6
?
Variant 8-132572310-A-G is Benign according to our data. Variant chr8-132572310-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 260274.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-132572310-A-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF11 | NM_012472.6 | c.1397T>C | p.Ile466Thr | missense_variant | 12/12 | ENST00000620350.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF11 | ENST00000620350.5 | c.1397T>C | p.Ile466Thr | missense_variant | 12/12 | 1 | NM_012472.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.151 AC: 22926AN: 152032Hom.: 2568 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
22926
AN:
152032
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0991 AC: 24690AN: 249022Hom.: 1789 AF XY: 0.0986 AC XY: 13275AN XY: 134602
GnomAD3 exomes
AF:
AC:
24690
AN:
249022
Hom.:
AF XY:
AC XY:
13275
AN XY:
134602
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0952 AC: 138902AN: 1459320Hom.: 7997 Cov.: 31 AF XY: 0.0958 AC XY: 69526AN XY: 725958
GnomAD4 exome
AF:
AC:
138902
AN:
1459320
Hom.:
Cov.:
31
AF XY:
AC XY:
69526
AN XY:
725958
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.151 AC: 22943AN: 152148Hom.: 2573 Cov.: 32 AF XY: 0.147 AC XY: 10924AN XY: 74378
GnomAD4 genome
?
AF:
AC:
22943
AN:
152148
Hom.:
Cov.:
32
AF XY:
AC XY:
10924
AN XY:
74378
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
333
ALSPAC
AF:
AC:
365
ESP6500AA
AF:
AC:
1297
ESP6500EA
AF:
AC:
832
ExAC
?
AF:
AC:
12803
Asia WGS
AF:
AC:
301
AN:
3476
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 19 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Primary ciliary dyskinesia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 08, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;D;D;D
Polyphen
0.97
.;D;D;.
Vest4
ClinPred
T
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