chr1-62555950-A-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001367561.1(DOCK7):āc.2471T>Cā(p.Ile824Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00219 in 1,613,854 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I824S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001367561.1 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 |
---|---|---|---|---|---|---|---|
DOCK7 | NM_001367561.1 | c.2471T>C | p.Ile824Thr | missense_variant | 21/50 | ENST00000635253.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK7 | ENST00000635253.2 | c.2471T>C | p.Ile824Thr | missense_variant | 21/50 | 5 | NM_001367561.1 |
Frequencies
GnomAD3 genomes AF: 0.0115 AC: 1744AN: 152210Hom.: 44 Cov.: 32
GnomAD3 exomes AF: 0.00302 AC: 758AN: 251164Hom.: 12 AF XY: 0.00223 AC XY: 303AN XY: 135760
GnomAD4 exome AF: 0.00122 AC: 1789AN: 1461526Hom.: 30 Cov.: 31 AF XY: 0.00105 AC XY: 767AN XY: 727054
GnomAD4 genome AF: 0.0115 AC: 1745AN: 152328Hom.: 44 Cov.: 32 AF XY: 0.0112 AC XY: 835AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 12, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 20, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 27, 2021 | - - |
Developmental and epileptic encephalopathy, 23 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at