rs10407660
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001256715.2(DNAAF3):c.323-17T>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,249,788 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.010 ( 29 hom., cov: 33)
Exomes 𝑓: 0.00092 ( 16 hom. )
Consequence
DNAAF3
NM_001256715.2 splice_polypyrimidine_tract, intron
NM_001256715.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.280
Genes affected
DNAAF3 (HGNC:30492): (dynein axonemal assembly factor 3) The protein encoded by this gene is required for the assembly of axonemal inner and outer dynein arms and plays a role in assembling dynein complexes for transport into cilia. Defects in this gene are a cause of primary ciliary dyskinesia type 2 (CILD2). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 19-55162307-A-C is Benign according to our data. Variant chr19-55162307-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 257686.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0102 (1550/152334) while in subpopulation AFR AF= 0.0347 (1444/41572). AF 95% confidence interval is 0.0332. There are 29 homozygotes in gnomad4. There are 712 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF3 | NM_001256715.2 | c.323-17T>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000524407.7 | |||
DNAAF3-AS1 | XR_007067344.1 | n.307-445A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF3 | ENST00000524407.7 | c.323-17T>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001256715.2 | A2 | |||
DNAAF3-AS1 | ENST00000591665.1 | n.1137-445A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0102 AC: 1551AN: 152216Hom.: 29 Cov.: 33
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GnomAD3 exomes AF: 0.00283 AC: 63AN: 22262Hom.: 1 AF XY: 0.00119 AC XY: 12AN XY: 10124
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GnomAD4 exome AF: 0.000920 AC: 1010AN: 1097454Hom.: 16 Cov.: 31 AF XY: 0.000855 AC XY: 443AN XY: 518200
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GnomAD4 genome ? AF: 0.0102 AC: 1550AN: 152334Hom.: 29 Cov.: 33 AF XY: 0.00956 AC XY: 712AN XY: 74486
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 13, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 07, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at