rs188496398
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001367479.1(DNAH14):c.5031C>G(p.Leu1677=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,549,856 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0030 ( 40 hom. )
Consequence
DNAH14
NM_001367479.1 synonymous
NM_001367479.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.289
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
Variant 1-225152718-C-G is Benign according to our data. Variant chr1-225152718-C-G is described in ClinVar as [Benign]. Clinvar id is 402651.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.289 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00299 (4173/1397686) while in subpopulation MID AF= 0.0338 (192/5686). AF 95% confidence interval is 0.0299. There are 40 homozygotes in gnomad4_exome. There are 2351 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH14 | NM_001367479.1 | c.5031C>G | p.Leu1677= | synonymous_variant | 33/86 | ENST00000682510.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH14 | ENST00000682510.1 | c.5031C>G | p.Leu1677= | synonymous_variant | 33/86 | NM_001367479.1 | P1 | ||
DNAH14 | ENST00000430092.5 | c.4980C>G | p.Leu1660= | synonymous_variant | 32/84 | 5 | |||
DNAH14 | ENST00000439375.6 | c.4980C>G | p.Leu1660= | synonymous_variant | 31/83 | 5 | |||
DNAH14 | ENST00000445597.6 | c.3750C>G | p.Leu1250= | synonymous_variant | 20/61 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00316 AC: 480AN: 152052Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00589 AC: 915AN: 155242Hom.: 15 AF XY: 0.00656 AC XY: 540AN XY: 82314
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GnomAD4 exome AF: 0.00299 AC: 4173AN: 1397686Hom.: 40 Cov.: 31 AF XY: 0.00341 AC XY: 2351AN XY: 689192
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
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: Silent variant not in splice consensus - |
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