rs2242241
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003974.4(DOK2):āc.1180T>Gā(p.Ser394Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 1,582,630 control chromosomes in the GnomAD database, including 184 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003974.4 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 |
---|---|---|---|---|---|---|---|
DOK2 | NM_003974.4 | c.1180T>G | p.Ser394Ala | missense_variant | 5/5 | ENST00000276420.9 | |
DOK2 | NM_001401272.1 | c.898T>G | p.Ser300Ala | missense_variant | 4/4 | ||
DOK2 | NM_001317800.2 | c.718T>G | p.Ser240Ala | missense_variant | 3/3 | ||
DOK2 | NM_201349.3 | c.718T>G | p.Ser240Ala | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOK2 | ENST00000276420.9 | c.1180T>G | p.Ser394Ala | missense_variant | 5/5 | 1 | NM_003974.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00826 AC: 1258AN: 152224Hom.: 54 Cov.: 32
GnomAD3 exomes AF: 0.0105 AC: 2369AN: 225874Hom.: 93 AF XY: 0.00821 AC XY: 998AN XY: 121532
GnomAD4 exome AF: 0.00280 AC: 4001AN: 1430288Hom.: 130 Cov.: 30 AF XY: 0.00248 AC XY: 1758AN XY: 708486
GnomAD4 genome ? AF: 0.00827 AC: 1260AN: 152342Hom.: 54 Cov.: 32 AF XY: 0.00991 AC XY: 738AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2019 | This variant is associated with the following publications: (PMID: 30206226) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at