rs201610914

Variant summary

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

The NM_004913.3(VPS9D1):​c.1532C>T​(p.Ala511Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,609,512 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00011 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00014 ( 1 hom. )

Consequence

VPS9D1
NM_004913.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.61
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=0.2202152).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VPS9D1NM_004913.3 linkc.1532C>T p.Ala511Val missense_variant Exon 12 of 15 ENST00000389386.8 NP_004904.2 Q9Y2B5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VPS9D1ENST00000389386.8 linkc.1532C>T p.Ala511Val missense_variant Exon 12 of 15 1 NM_004913.3 ENSP00000374037.3 Q9Y2B5-1
VPS9D1ENST00000561976.5 linkc.1322C>T p.Ala441Val missense_variant Exon 11 of 14 1 ENSP00000454244.1 H3BM58
VPS9D1ENST00000565023.1 linkc.332C>T p.Ala111Val missense_variant Exon 3 of 6 5 ENSP00000455792.1 H3BQI2

Frequencies

GnomAD3 genomes
AF:
0.000105
AC:
16
AN:
152150
Hom.:
0
Cov.:
31
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:
0.000191
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000112
AC:
27
AN:
240782
Hom.:
0
AF XY:
0.000121
AC XY:
16
AN XY:
131880
show subpopulations
Gnomad AFR exome
AF:
0.0000679
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000560
Gnomad SAS exome
AF:
0.0000330
Gnomad FIN exome
AF:
0.0000980
Gnomad NFE exome
AF:
0.000186
Gnomad OTH exome
AF:
0.000340
GnomAD4 exome
AF:
0.000135
AC:
197
AN:
1457362
Hom.:
1
Cov.:
32
AF XY:
0.000121
AC XY:
88
AN XY:
725060
show subpopulations
Gnomad4 AFR exome
AF:
0.0000598
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000349
Gnomad4 FIN exome
AF:
0.000235
Gnomad4 NFE exome
AF:
0.000152
Gnomad4 OTH exome
AF:
0.000149
GnomAD4 genome
AF:
0.000105
AC:
16
AN:
152150
Hom.:
0
Cov.:
31
AF XY:
0.000121
AC XY:
9
AN XY:
74314
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:
0.000191
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000904
Hom.:
0
Bravo
AF:
0.0000756
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000243
AC:
2
ExAC
AF:
0.0000828
AC:
10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.099
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
14
DANN
Uncertain
1.0
DEOGEN2
Benign
0.030
.;T
Eigen
Benign
-0.24
Eigen_PC
Benign
-0.36
FATHMM_MKL
Benign
0.37
N
LIST_S2
Benign
0.79
T;T
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.22
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.5
.;M
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-1.2
N;N
REVEL
Benign
0.063
Sift
Benign
0.086
T;T
Sift4G
Uncertain
0.032
D;D
Polyphen
0.86
.;P
Vest4
0.27
MVP
0.38
MPC
0.21
ClinPred
0.047
T
GERP RS
4.1
Varity_R
0.065
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs201610914; hg19: chr16-89775700; COSMIC: COSV101231951; COSMIC: COSV101231951; API