chr7-785575-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_017802.4(DNAAF5):c.2490C>T(p.Ala830Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,262 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 0.000099 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000035 ( 0 hom. )
Consequence
DNAAF5
NM_017802.4 synonymous
NM_017802.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.27
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 7-785575-C-T is Benign according to our data. Variant chr7-785575-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 260934.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.27 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0000986 (15/152194) while in subpopulation AMR AF= 0.00072 (11/15274). AF 95% confidence interval is 0.000403. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF5 | NM_017802.4 | c.2490C>T | p.Ala830Ala | synonymous_variant | 13/13 | ENST00000297440.11 | NP_060272.3 | |
DNAAF5 | XM_024446813.2 | c.2298C>T | p.Ala766Ala | synonymous_variant | 12/12 | XP_024302581.1 | ||
DNAAF5 | NR_075098.2 | n.2450C>T | non_coding_transcript_exon_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF5 | ENST00000297440.11 | c.2490C>T | p.Ala830Ala | synonymous_variant | 13/13 | 1 | NM_017802.4 | ENSP00000297440.6 | ||
DNAAF5 | ENST00000403952.3 | c.765C>T | p.Ala255Ala | synonymous_variant | 6/6 | 1 | ENSP00000384884.3 | |||
DNAAF5 | ENST00000440747.5 | c.1893C>T | p.Ala631Ala | synonymous_variant | 13/13 | 2 | ENSP00000403165.1 | |||
DNAAF5 | ENST00000461576.1 | n.*2C>T | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152194Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250830Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135748
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GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461068Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 726840
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GnomAD4 genome AF: 0.0000986 AC: 15AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74338
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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