rs200128185
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_004946.3(DOCK2):c.5445G>A(p.Ser1815=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000892 in 1,614,132 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1815S) has been classified as Likely benign.
Frequency
Consequence
NM_004946.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK2 | NM_004946.3 | c.5445G>A | p.Ser1815= | synonymous_variant | 52/52 | ENST00000520908.7 | |
DOCK2 | NR_156756.1 | n.5548G>A | non_coding_transcript_exon_variant | 53/53 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK2 | ENST00000520908.7 | c.5445G>A | p.Ser1815= | synonymous_variant | 52/52 | 2 | NM_004946.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00105 AC: 160AN: 152152Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00195 AC: 489AN: 251198Hom.: 2 AF XY: 0.00191 AC XY: 259AN XY: 135798
GnomAD4 exome AF: 0.000875 AC: 1279AN: 1461862Hom.: 1 Cov.: 31 AF XY: 0.000872 AC XY: 634AN XY: 727228
GnomAD4 genome ? AF: 0.00105 AC: 160AN: 152270Hom.: 1 Cov.: 32 AF XY: 0.00103 AC XY: 77AN XY: 74464
ClinVar
Submissions by phenotype
DOCK2 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
DOCK2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 27, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at