chr5-170082811-G-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_004946.3(DOCK2):c.5446G>T(p.Ala1816Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,614,154 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004946.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK2 | NM_004946.3 | c.5446G>T | p.Ala1816Ser | missense_variant | 52/52 | ENST00000520908.7 | |
DOCK2 | NR_156756.1 | n.5549G>T | non_coding_transcript_exon_variant | 53/53 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK2 | ENST00000520908.7 | c.5446G>T | p.Ala1816Ser | missense_variant | 52/52 | 2 | NM_004946.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00151 AC: 230AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00144 AC: 361AN: 251230Hom.: 0 AF XY: 0.00144 AC XY: 195AN XY: 135806
GnomAD4 exome AF: 0.00250 AC: 3660AN: 1461848Hom.: 7 Cov.: 31 AF XY: 0.00235 AC XY: 1711AN XY: 727226
GnomAD4 genome AF: 0.00151 AC: 230AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.00136 AC XY: 101AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2021 | - - |
DOCK2 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at