chr16-89708467-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004913.3(VPS9D1):c.1762G>A(p.Val588Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,613,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000072 ( 0 hom. )
Consequence
VPS9D1
NM_004913.3 missense
NM_004913.3 missense
Scores
10
9
Clinical Significance
Conservation
PhyloP100: 2.42
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;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS9D1 | NM_004913.3 | c.1762G>A | p.Val588Met | missense_variant | 14/15 | ENST00000389386.8 | NP_004904.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.1762G>A | p.Val588Met | missense_variant | 14/15 | 1 | NM_004913.3 | ENSP00000374037 | A2 | |
VPS9D1 | ENST00000561976.5 | c.1552G>A | p.Val518Met | missense_variant | 13/14 | 1 | ENSP00000454244 | P2 | ||
VPS9D1 | ENST00000565023.1 | c.565G>A | p.Val189Met | missense_variant | 5/6 | 5 | ENSP00000455792 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152256Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000980 AC: 24AN: 244880Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 133736
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GnomAD4 exome AF: 0.0000719 AC: 105AN: 1460714Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 726674
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152374Hom.: 0 Cov.: 34 AF XY: 0.0000671 AC XY: 5AN XY: 74508
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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 | Jul 14, 2021 | The c.1762G>A (p.V588M) alteration is located in exon 14 (coding exon 14) of the VPS9D1 gene. This alteration results from a G to A substitution at nucleotide position 1762, causing the valine (V) at amino acid position 588 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Polyphen
0.99
.;D
Vest4
MVP
MPC
0.60
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
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