chr13-98829318-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_001366683.2(DOCK9):c.4954G>A(p.Asp1652Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,611,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
DOCK9
NM_001366683.2 missense
NM_001366683.2 missense
Scores
4
3
6
Clinical Significance
Conservation
PhyloP100: 7.49
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, DOCK9
BP4
?
Computational evidence support a benign effect (MetaRNN=0.39500892).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK9 | NM_001366683.2 | c.4954G>A | p.Asp1652Asn | missense_variant | 43/53 | ENST00000682017.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK9 | ENST00000682017.1 | c.4954G>A | p.Asp1652Asn | missense_variant | 43/53 | NM_001366683.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245140Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133030
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GnomAD4 exome AF: 0.0000253 AC: 37AN: 1459810Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 725930
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.4888G>A (p.D1630N) alteration is located in exon 43 (coding exon 43) of the DOCK9 gene. This alteration results from a G to A substitution at nucleotide position 4888, causing the aspartic acid (D) at amino acid position 1630 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
Polyphen
0.97, 0.86
.;D;.;.;P
Vest4
0.83, 0.79
MVP
MPC
1.0
ClinPred
D
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at