rs112998568
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_001206927.2(DNAH8):c.13214+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000393 in 1,580,898 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 1 hom. )
Consequence
DNAH8
NM_001206927.2 intron
NM_001206927.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00300
Genes affected
DNAH8 (HGNC:2952): (dynein axonemal heavy chain 8) The protein encoded by this gene is a heavy chain of an axonemal dynein involved in sperm and respiratory cilia motility. Axonemal dyneins generate force through hydrolysis of ATP and binding to microtubules. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 6-38990182-T-C is Benign according to our data. Variant chr6-38990182-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 238636.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00199 (303/152330) while in subpopulation AFR AF= 0.00686 (285/41568). AF 95% confidence interval is 0.0062. There are 1 homozygotes in gnomad4. There are 138 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH8 | NM_001206927.2 | c.13214+10T>C | intron_variant | ENST00000327475.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH8 | ENST00000327475.11 | c.13214+10T>C | intron_variant | 5 | NM_001206927.2 | P2 | |||
DNAH8 | ENST00000359357.7 | c.12563+10T>C | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00194 AC: 296AN: 152212Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000582 AC: 132AN: 226692Hom.: 0 AF XY: 0.000449 AC XY: 55AN XY: 122552
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GnomAD4 exome AF: 0.000223 AC: 318AN: 1428568Hom.: 1 Cov.: 27 AF XY: 0.000207 AC XY: 147AN XY: 710648
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
DNAH8-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 12, 2019 | This variant is classified as likely 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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Name
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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