rs691225
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_173628.4(DNAH17):c.8907C>T(p.Ser2969=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 1,611,012 control chromosomes in the GnomAD database, including 468,641 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.67 ( 36293 hom., cov: 31)
Exomes 𝑓: 0.77 ( 432348 hom. )
Consequence
DNAH17
NM_173628.4 synonymous
NM_173628.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.209
Genes affected
DNAH17 (HGNC:2946): (dynein axonemal heavy chain 17) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. DNAH17 is a heavy chain associated with axonemal dynein (Milisav and Affara, 1998 [PubMed 9545504]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 17-78466688-G-A is Benign according to our data. Variant chr17-78466688-G-A is described in ClinVar as [Benign]. Clinvar id is 402677.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.209 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH17 | NM_173628.4 | c.8907C>T | p.Ser2969= | synonymous_variant | 56/81 | ENST00000389840.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH17 | ENST00000389840.7 | c.8907C>T | p.Ser2969= | synonymous_variant | 56/81 | 5 | NM_173628.4 | P1 | |
DNAH17 | ENST00000586052.5 | n.2289C>T | non_coding_transcript_exon_variant | 12/35 | 5 | ||||
DNAH17 | ENST00000591369.5 | c.510C>T | p.Ser170= | synonymous_variant, NMD_transcript_variant | 3/28 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.670 AC: 101790AN: 151894Hom.: 36283 Cov.: 31
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GnomAD3 exomes AF: 0.738 AC: 181658AN: 246148Hom.: 68407 AF XY: 0.737 AC XY: 98620AN XY: 133798
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GnomAD4 exome AF: 0.766 AC: 1117628AN: 1459000Hom.: 432348 Cov.: 54 AF XY: 0.763 AC XY: 553377AN XY: 725678
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GnomAD4 genome ? AF: 0.670 AC: 101822AN: 152012Hom.: 36293 Cov.: 31 AF XY: 0.670 AC XY: 49750AN XY: 74294
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
DNAH17-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at