chr4-3492953-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_173660.5(DOK7):c.967C>T(p.Arg323Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00149 in 1,553,432 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R323H) has been classified as Uncertain significance.
Frequency
Consequence
NM_173660.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK7 | NM_173660.5 | c.967C>T | p.Arg323Cys | missense_variant | 7/7 | ENST00000340083.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK7 | ENST00000340083.6 | c.967C>T | p.Arg323Cys | missense_variant | 7/7 | 1 | NM_173660.5 | P1 | |
DOK7 | ENST00000643608.1 | c.535C>T | p.Arg179Cys | missense_variant | 5/8 | ||||
DOK7 | ENST00000515886.5 | c.37C>T | p.Arg13Cys | missense_variant | 4/4 | 2 | |||
DOK7 | ENST00000507039.5 | c.*188C>T | 3_prime_UTR_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00765 AC: 1164AN: 152220Hom.: 20 Cov.: 34
GnomAD3 exomes AF: 0.00185 AC: 283AN: 153362Hom.: 5 AF XY: 0.00146 AC XY: 122AN XY: 83426
GnomAD4 exome AF: 0.000821 AC: 1150AN: 1401094Hom.: 13 Cov.: 111 AF XY: 0.000702 AC XY: 486AN XY: 692378
GnomAD4 genome AF: 0.00765 AC: 1165AN: 152338Hom.: 20 Cov.: 34 AF XY: 0.00728 AC XY: 542AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Fetal akinesia deformation sequence 1;C1850792:Congenital myasthenic syndrome 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 20, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at