rs201554395

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_017802.4(DNAAF5):​c.1024+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000563 in 1,226,662 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 (★).

Frequency

Genomes: 𝑓 0.000065 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )

Consequence

DNAAF5
NM_017802.4 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0220
Variant links:
Genes affected
DNAAF5 (HGNC:26013): (dynein axonemal assembly factor 5) The protein encoded by this gene is essential for the preassembly or stability of axonemal dynein arms, and is found only in organisms with motile cilia and flagella. Mutations in this gene are associated with primary ciliary dyskinesia-18, a disorder characterized by abnormalities of motile cilia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2013]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 7-741476-G-A is Benign according to our data. Variant chr7-741476-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2914443.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAAF5NM_017802.4 linkc.1024+11G>A intron_variant Intron 4 of 12 ENST00000297440.11 NP_060272.3 Q86Y56-1B3KPE2
DNAAF5XM_024446813.2 linkc.1024+11G>A intron_variant Intron 4 of 11 XP_024302581.1
DNAAF5NR_075098.2 linkn.984+11G>A intron_variant Intron 4 of 12

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAAF5ENST00000297440.11 linkc.1024+11G>A intron_variant Intron 4 of 12 1 NM_017802.4 ENSP00000297440.6 Q86Y56-1
DNAAF5ENST00000440747.5 linkc.427+11G>A intron_variant Intron 4 of 12 2 ENSP00000403165.1 H0Y650
DNAAF5ENST00000437419.5 linkc.340+11G>A intron_variant Intron 3 of 4 5 ENSP00000410788.1 H7C3B1
DNAAF5ENST00000438961.1 linkn.493+11G>A intron_variant Intron 4 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.0000646
AC:
9
AN:
139238
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000516
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000109
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.0000627
AC:
11
AN:
175406
AF XY:
0.0000432
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000358
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000693
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000552
AC:
60
AN:
1087424
Hom.:
0
Cov.:
20
AF XY:
0.0000576
AC XY:
31
AN XY:
537850
show subpopulations
Gnomad4 AFR exome
AF:
0.00
AC:
0
AN:
24782
Gnomad4 AMR exome
AF:
0.0000336
AC:
1
AN:
29784
Gnomad4 ASJ exome
AF:
0.00
AC:
0
AN:
16112
Gnomad4 EAS exome
AF:
0.000352
AC:
6
AN:
17040
Gnomad4 SAS exome
AF:
0.0000397
AC:
3
AN:
75646
Gnomad4 FIN exome
AF:
0.00
AC:
0
AN:
32152
Gnomad4 NFE exome
AF:
0.0000578
AC:
49
AN:
848248
Gnomad4 Remaining exome
AF:
0.0000248
AC:
1
AN:
40358
Heterozygous variant carriers
0
3
7
10
14
17
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000646
AC:
9
AN:
139238
Hom.:
0
Cov.:
32
AF XY:
0.0000297
AC XY:
2
AN XY:
67322
show subpopulations
Gnomad4 AFR
AF:
0.0000516
AC:
0.0000516076
AN:
0.0000516076
Gnomad4 AMR
AF:
0.00
AC:
0
AN:
0
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 SAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 FIN
AF:
0.00
AC:
0
AN:
0
Gnomad4 NFE
AF:
0.000109
AC:
0.000109269
AN:
0.000109269
Gnomad4 OTH
AF:
0.00
AC:
0
AN:
0
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000216
Hom.:
0
Bravo
AF:
0.0000567

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Primary ciliary dyskinesia Benign:1
Oct 27, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.9
DANN
Benign
0.45
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201554395; hg19: chr7-781113; API