chr4-3493129-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_173660.5(DOK7):c.1143C>T(p.Pro381Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00321 in 1,594,468 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_173660.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DOK7 | ENST00000340083.6 | c.1143C>T | p.Pro381Pro | synonymous_variant | Exon 7 of 7 | 1 | NM_173660.5 | ENSP00000344432.5 | ||
DOK7 | ENST00000643608.1 | c.711C>T | p.Pro237Pro | synonymous_variant | Exon 5 of 8 | ENSP00000495701.1 | ||||
DOK7 | ENST00000515886.5 | c.213C>T | p.Pro71Pro | synonymous_variant | Exon 4 of 4 | 2 | ENSP00000492194.1 | |||
DOK7 | ENST00000507039.5 | c.*364C>T | 3_prime_UTR_variant | Exon 7 of 7 | 2 | ENSP00000423614.1 |
Frequencies
GnomAD3 genomes AF: 0.0132 AC: 2016AN: 152194Hom.: 35 Cov.: 34
GnomAD3 exomes AF: 0.00388 AC: 806AN: 207784Hom.: 18 AF XY: 0.00321 AC XY: 368AN XY: 114522
GnomAD4 exome AF: 0.00215 AC: 3100AN: 1442156Hom.: 45 Cov.: 113 AF XY: 0.00212 AC XY: 1518AN XY: 716400
GnomAD4 genome AF: 0.0133 AC: 2022AN: 152312Hom.: 35 Cov.: 34 AF XY: 0.0125 AC XY: 930AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:4
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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. -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Fetal akinesia deformation sequence 1;C1850792:Congenital myasthenic syndrome 10 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at