chr19-11215909-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_020812.4(DOCK6):c.3913C>T(p.Arg1305Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00972 in 1,613,744 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1305H) has been classified as Uncertain significance.
Frequency
Consequence
NM_020812.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK6 | NM_020812.4 | c.3913C>T | p.Arg1305Cys | missense_variant | 31/48 | ENST00000294618.12 | |
LOC105372273 | NR_134909.1 | n.538-228G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK6 | ENST00000294618.12 | c.3913C>T | p.Arg1305Cys | missense_variant | 31/48 | 1 | NM_020812.4 | A2 | |
ENST00000588634.1 | n.538-228G>A | intron_variant, non_coding_transcript_variant | 4 | ||||||
DOCK6 | ENST00000587656.6 | c.4018C>T | p.Arg1340Cys | missense_variant | 32/49 | 5 | P3 | ||
DOCK6 | ENST00000588429.1 | n.268C>T | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00783 AC: 1190AN: 152016Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00846 AC: 2109AN: 249286Hom.: 17 AF XY: 0.00861 AC XY: 1164AN XY: 135248
GnomAD4 exome AF: 0.00992 AC: 14496AN: 1461610Hom.: 94 Cov.: 30 AF XY: 0.00989 AC XY: 7190AN XY: 727076
GnomAD4 genome AF: 0.00782 AC: 1190AN: 152134Hom.: 7 Cov.: 32 AF XY: 0.00826 AC XY: 614AN XY: 74358
ClinVar
Submissions by phenotype
not provided Benign:6
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 10, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 19, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | DOCK6: BS1, BS2 - |
Adams-Oliver syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 16, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at