rs147185207
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS1
The NM_173660.5(DOK7):c.1406C>A(p.Pro469His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,594,708 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00032 ( 5 hom., cov: 35)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
DOK7
NM_173660.5 missense
NM_173660.5 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 1.02
Genes affected
DOK7 (HGNC:26594): (docking protein 7) The protein encoded by this gene is essential for neuromuscular synaptogenesis. The protein functions in aneural activation of muscle-specific receptor kinase, which is required for postsynaptic differentiation, and in the subsequent clustering of the acetylcholine receptor in myotubes. This protein can also induce autophosphorylation of muscle-specific receptor kinase. Mutations in this gene are a cause of familial limb-girdle myasthenia autosomal recessive, which is also known as congenital myasthenic syndrome type 1B. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008318365).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000322 (49/152358) while in subpopulation EAS AF= 0.00482 (25/5192). AF 95% confidence interval is 0.00335. There are 5 homozygotes in gnomad4. There are 25 alleles in male gnomad4 subpopulation. Median coverage is 35. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK7 | NM_173660.5 | c.1406C>A | p.Pro469His | missense_variant | 7/7 | ENST00000340083.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK7 | ENST00000340083.6 | c.1406C>A | p.Pro469His | missense_variant | 7/7 | 1 | NM_173660.5 | P1 | |
DOK7 | ENST00000643608.1 | c.974C>A | p.Pro325His | missense_variant | 5/8 | ||||
DOK7 | ENST00000515886.5 | c.476C>A | p.Pro159His | missense_variant | 4/4 | 2 | |||
DOK7 | ENST00000507039.5 | c.*627C>A | 3_prime_UTR_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152240Hom.: 0 Cov.: 35
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000357 AC: 72AN: 201940Hom.: 0 AF XY: 0.000332 AC XY: 37AN XY: 111586
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GnomAD4 exome AF: 0.000148 AC: 214AN: 1442350Hom.: 0 Cov.: 89 AF XY: 0.000145 AC XY: 104AN XY: 716066
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GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152358Hom.: 5 Cov.: 35 AF XY: 0.000336 AC XY: 25AN XY: 74508
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3478
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 28, 2019 | - - |
Fetal akinesia deformation sequence 1;C1850792:Congenital myasthenic syndrome 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;.
REVEL
Uncertain
Sift
Benign
T;.;.
Sift4G
Uncertain
D;.;.
Polyphen
D;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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