GeneBe

16-84150372-G-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_178452.6(DNAAF1):​c.352+30G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000147 in 1,358,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

DNAAF1
NM_178452.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.786

Publications

0 publications found
Variant links:
Genes affected
DNAAF1 (HGNC:30539): (dynein axonemal assembly factor 1) The protein encoded by this gene is cilium-specific and is required for the stability of the ciliary architecture. It is involved in the regulation of microtubule-based cilia and actin-based brush border microvilli. Mutations in this gene are associated with primary ciliary dyskinesia-13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
DNAAF1 Gene-Disease associations (from GenCC):
  • primary ciliary dyskinesia 13
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, PanelApp Australia
  • primary ciliary dyskinesia
    Inheritance: 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 -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAAF1NM_178452.6 linkc.352+30G>C intron_variant Intron 3 of 11 ENST00000378553.10 NP_848547.4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAAF1ENST00000378553.10 linkc.352+30G>C intron_variant Intron 3 of 11 1 NM_178452.6 ENSP00000367815.5
DNAAF1ENST00000567918.5 linkn.352+30G>C intron_variant Intron 3 of 6 1 ENSP00000455154.1
DNAAF1ENST00000563093.5 linkn.352+30G>C intron_variant Intron 3 of 10 2 ENSP00000457373.1
DNAAF1ENST00000570298.5 linkn.506+30G>C intron_variant Intron 3 of 10 2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000147
AC:
2
AN:
1358530
Hom.:
0
Cov.:
21
AF XY:
0.00000147
AC XY:
1
AN XY:
681954
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
31272
American (AMR)
AF:
0.00
AC:
0
AN:
44588
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25520
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39180
South Asian (SAS)
AF:
0.00
AC:
0
AN:
84264
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53288
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5600
European-Non Finnish (NFE)
AF:
0.00000196
AC:
2
AN:
1017826
Other (OTH)
AF:
0.00
AC:
0
AN:
56992
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

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
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.16
DANN
Benign
0.50
PhyloP100
-0.79

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

Other links and lift over

dbSNP: rs78056463; hg19: chr16-84183977; API