NM_173660.5:c.1469C>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.1469C>T(p.Ser490Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,609,980 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DOK7 | ENST00000340083.6 | c.1469C>T | p.Ser490Leu | missense_variant | Exon 7 of 7 | 1 | NM_173660.5 | ENSP00000344432.5 | ||
DOK7 | ENST00000643608.1 | c.1037C>T | p.Ser346Leu | missense_variant | Exon 5 of 8 | ENSP00000495701.1 | ||||
DOK7 | ENST00000515886.5 | c.539C>T | p.Ser180Leu | missense_variant | Exon 4 of 4 | 2 | ENSP00000492194.1 | |||
DOK7 | ENST00000507039.5 | c.*690C>T | 3_prime_UTR_variant | Exon 7 of 7 | 2 | ENSP00000423614.1 |
Frequencies
GnomAD3 genomes AF: 0.00257 AC: 392AN: 152244Hom.: 4 Cov.: 35
GnomAD3 exomes AF: 0.00528 AC: 1242AN: 235078Hom.: 11 AF XY: 0.00473 AC XY: 612AN XY: 129510
GnomAD4 exome AF: 0.00185 AC: 2699AN: 1457618Hom.: 25 Cov.: 88 AF XY: 0.00176 AC XY: 1275AN XY: 724860
GnomAD4 genome AF: 0.00258 AC: 393AN: 152362Hom.: 4 Cov.: 35 AF XY: 0.00282 AC XY: 210AN XY: 74504
ClinVar
Submissions by phenotype
not specified Benign:1
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Fetal akinesia deformation sequence 1;C1850792:Congenital myasthenic syndrome 10 Benign:1
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Fetal akinesia deformation sequence 3 Benign:1
This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at