17-11598497-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000262442.9(DNAH9):c.-2C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 1,366,578 control chromosomes in the GnomAD database, including 193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0041 ( 23 hom., cov: 32)
Exomes 𝑓: 0.0033 ( 170 hom. )
Consequence
DNAH9
ENST00000262442.9 5_prime_UTR
ENST00000262442.9 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.147
Genes affected
DNAH9 (HGNC:2953): (dynein axonemal heavy chain 9) This gene encodes the heavy chain subunit of axonemal dynein, a large multi-subunit molecular motor. Axonemal dynein attaches to microtubules and hydrolyzes ATP to mediate the movement of cilia and flagella. The gene expresses at least two transcript variants; additional variants have been described, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 17-11598497-C-T is Benign according to our data. Variant chr17-11598497-C-T is described in ClinVar as [Benign]. Clinvar id is 3044413.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0748 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH9 | NM_001372.4 | c.-2C>T | 5_prime_UTR_variant | 1/69 | ENST00000262442.9 | NP_001363.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH9 | ENST00000262442.9 | c.-2C>T | 5_prime_UTR_variant | 1/69 | 1 | NM_001372.4 | ENSP00000262442 | P1 | ||
DNAH9 | ENST00000579406.1 | n.26C>T | non_coding_transcript_exon_variant | 1/8 | 1 | |||||
DNAH9 | ENST00000579828.5 | c.-2C>T | 5_prime_UTR_variant | 1/4 | 2 | ENSP00000463782 | ||||
DNAH9 | ENST00000454412.6 | upstream_gene_variant | 5 | ENSP00000414874 |
Frequencies
GnomAD3 genomes AF: 0.00406 AC: 617AN: 152150Hom.: 23 Cov.: 32
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GnomAD3 exomes AF: 0.0182 AC: 87AN: 4784Hom.: 5 AF XY: 0.0174 AC XY: 47AN XY: 2696
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GnomAD4 exome AF: 0.00326 AC: 3954AN: 1214310Hom.: 170 Cov.: 33 AF XY: 0.00346 AC XY: 2038AN XY: 589494
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GnomAD4 genome AF: 0.00407 AC: 619AN: 152268Hom.: 23 Cov.: 32 AF XY: 0.00430 AC XY: 320AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
DNAH9-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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