rs11077375
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_173628.4(DNAH17):c.5904-15C>T 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 0.26 in 1,585,328 control chromosomes in the GnomAD database, including 55,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.23 ( 4302 hom., cov: 34)
Exomes 𝑓: 0.26 ( 50734 hom. )
Consequence
DNAH17
NM_173628.4 splice_polypyrimidine_tract, intron
NM_173628.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.469
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 17-78495112-G-A is Benign according to our data. Variant chr17-78495112-G-A is described in ClinVar as [Benign]. Clinvar id is 402684.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH17 | NM_173628.4 | c.5904-15C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000389840.7 | |||
DNAH17-AS1 | NR_102401.1 | n.769+915G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH17 | ENST00000389840.7 | c.5904-15C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_173628.4 | P1 | |||
DNAH17-AS1 | ENST00000591373.2 | n.769+915G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.230 AC: 35045AN: 152062Hom.: 4296 Cov.: 34
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GnomAD3 exomes AF: 0.276 AC: 59254AN: 214656Hom.: 8442 AF XY: 0.277 AC XY: 32269AN XY: 116412
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GnomAD4 exome AF: 0.263 AC: 376669AN: 1433148Hom.: 50734 Cov.: 37 AF XY: 0.265 AC XY: 188326AN XY: 709688
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GnomAD4 genome ? AF: 0.230 AC: 35058AN: 152180Hom.: 4302 Cov.: 34 AF XY: 0.232 AC XY: 17236AN XY: 74416
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ClinVar
Significance: Benign
Submissions summary: Benign:2
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 - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 11, 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