rs12742757
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001367479.1(DNAH14):c.10746T>A(p.Ile3582=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 1,551,380 control chromosomes in the GnomAD database, including 7,724 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 1173 hom., cov: 32)
Exomes 𝑓: 0.085 ( 6551 hom. )
Consequence
DNAH14
NM_001367479.1 synonymous
NM_001367479.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.813
Genes affected
DNAH14 (HGNC:2945): (dynein axonemal heavy chain 14) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. Two major classes of dyneins, axonemal and cytoplasmic, have been identified. DNAH14 is an axonemal dynein heavy chain (DHC) (Vaughan et al., 1996 [PubMed 8812413]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 1-225346029-T-A is Benign according to our data. Variant chr1-225346029-T-A is described in ClinVar as [Benign]. Clinvar id is 402658.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.813 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH14 | NM_001367479.1 | c.10746T>A | p.Ile3582= | synonymous_variant | 70/86 | ENST00000682510.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH14 | ENST00000682510.1 | c.10746T>A | p.Ile3582= | synonymous_variant | 70/86 | NM_001367479.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17255AN: 151948Hom.: 1170 Cov.: 32
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GnomAD3 exomes AF: 0.120 AC: 18615AN: 155208Hom.: 1588 AF XY: 0.112 AC XY: 9217AN XY: 82312
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GnomAD4 exome AF: 0.0848 AC: 118628AN: 1399316Hom.: 6551 Cov.: 42 AF XY: 0.0841 AC XY: 58012AN XY: 690176
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GnomAD4 genome ? AF: 0.114 AC: 17275AN: 152064Hom.: 1173 Cov.: 32 AF XY: 0.119 AC XY: 8819AN XY: 74346
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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 28, 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 | Feb 11, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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