chr16-89710631-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004913.3(VPS9D1):ā€‹c.1213C>Gā€‹(p.Leu405Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,610,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00016 ( 0 hom., cov: 32)
Exomes š‘“: 0.00019 ( 0 hom. )

Consequence

VPS9D1
NM_004913.3 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.299
Variant links:
Genes affected
VPS9D1 (HGNC:13526): (VPS9 domain containing 1) Enables identical protein binding activity. Predicted to be involved in ATP synthesis coupled proton transport. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08875105).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
VPS9D1NM_004913.3 linkuse as main transcriptc.1213C>G p.Leu405Val missense_variant 10/15 ENST00000389386.8 NP_004904.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VPS9D1ENST00000389386.8 linkuse as main transcriptc.1213C>G p.Leu405Val missense_variant 10/151 NM_004913.3 ENSP00000374037 A2Q9Y2B5-1
VPS9D1ENST00000561976.5 linkuse as main transcriptc.1003C>G p.Leu335Val missense_variant 9/141 ENSP00000454244 P2
VPS9D1ENST00000565023.1 linkuse as main transcriptc.13C>G p.Leu5Val missense_variant 1/65 ENSP00000455792

Frequencies

GnomAD3 genomes
AF:
0.000158
AC:
24
AN:
152210
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000309
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000491
AC:
12
AN:
244550
Hom.:
0
AF XY:
0.0000449
AC XY:
6
AN XY:
133712
show subpopulations
Gnomad AFR exome
AF:
0.0000668
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000472
Gnomad NFE exome
AF:
0.0000911
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000187
AC:
272
AN:
1457982
Hom.:
0
Cov.:
32
AF XY:
0.000174
AC XY:
126
AN XY:
724802
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000574
Gnomad4 NFE exome
AF:
0.000215
Gnomad4 OTH exome
AF:
0.000482
GnomAD4 genome
AF:
0.000158
AC:
24
AN:
152210
Hom.:
0
Cov.:
32
AF XY:
0.000148
AC XY:
11
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0000724
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000309
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000248
Hom.:
0
Bravo
AF:
0.000128
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000248
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000497
AC:
6
EpiCase
AF:
0.000491
EpiControl
AF:
0.000178

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 submitterclinical testingAmbry GeneticsOct 29, 2021The c.1213C>G (p.L405V) alteration is located in exon 10 (coding exon 10) of the VPS9D1 gene. This alteration results from a C to G substitution at nucleotide position 1213, causing the leucine (L) at amino acid position 405 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.070
BayesDel_addAF
Benign
-0.34
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
12
DANN
Uncertain
0.99
DEOGEN2
Benign
0.018
.;T
Eigen
Benign
-0.37
Eigen_PC
Benign
-0.51
FATHMM_MKL
Benign
0.13
N
LIST_S2
Benign
0.42
T;T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.089
T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.4
.;M
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-0.20
N;N
REVEL
Benign
0.048
Sift
Benign
0.24
T;T
Sift4G
Benign
0.41
T;T
Polyphen
0.0020
.;B
Vest4
0.21
MVP
0.16
MPC
0.20
ClinPred
0.041
T
GERP RS
0.81
Varity_R
0.045
gMVP
0.16

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs374855421; hg19: chr16-89777039; API