rs574117710
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The ENST00000455045.5(DNAAF3):c.-356G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,844 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 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
DNAAF3
ENST00000455045.5 5_prime_UTR
ENST00000455045.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.264
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 -10 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
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Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 19-55166625-C-G is Benign according to our data. Variant chr19-55166625-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 416071.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF3-AS1 | XR_007067344.1 | n.1163C>G | non_coding_transcript_exon_variant | 4/4 | |||
DNAAF3 | NM_001256715.2 | upstream_gene_variant | ENST00000524407.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF3-AS1 | ENST00000591665.1 | n.1186+3824C>G | intron_variant, non_coding_transcript_variant | 2 | |||||
DNAAF3 | ENST00000524407.7 | upstream_gene_variant | 1 | NM_001256715.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152194Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000482 AC: 12AN: 249104Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135164
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GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461532Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727038
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GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74466
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2021 | This alteration is classified as likely 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 11, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at