chr4-3493264-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_173660.5(DOK7):c.1278C>T(p.Pro426=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00251 in 1,611,556 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P426P) has been classified as Likely benign.
Frequency
Consequence
NM_173660.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOK7 | NM_173660.5 | c.1278C>T | p.Pro426= | synonymous_variant | 7/7 | ENST00000340083.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK7 | ENST00000340083.6 | c.1278C>T | p.Pro426= | synonymous_variant | 7/7 | 1 | NM_173660.5 | P1 | |
DOK7 | ENST00000643608.1 | c.846C>T | p.Pro282= | synonymous_variant | 5/8 | ||||
DOK7 | ENST00000515886.5 | c.348C>T | p.Pro116= | synonymous_variant | 4/4 | 2 | |||
DOK7 | ENST00000507039.5 | c.*499C>T | 3_prime_UTR_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00174 AC: 265AN: 152228Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00180 AC: 423AN: 235508Hom.: 3 AF XY: 0.00181 AC XY: 235AN XY: 129518
GnomAD4 exome AF: 0.00259 AC: 3781AN: 1459210Hom.: 8 Cov.: 96 AF XY: 0.00249 AC XY: 1804AN XY: 725846
GnomAD4 genome AF: 0.00174 AC: 265AN: 152346Hom.: 1 Cov.: 34 AF XY: 0.00169 AC XY: 126AN XY: 74492
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 16, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | DOK7: BP4, BP7, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 19, 2021 | - - |
Fetal akinesia deformation sequence 1;C1850792:Congenital myasthenic syndrome 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at