GeneBe

rs769779958

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_030796.5(VOPP1):​c.391G>T​(p.Gly131Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G131R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 20)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

VOPP1
NM_030796.5 missense

Scores

6
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.94

Publications

0 publications found
Variant links:
Genes affected
VOPP1 (HGNC:34518): (VOPP1 WW domain binding protein) Located in cytoplasmic vesicle membrane and endosome. Is integral component of organelle membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.17982832).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030796.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VOPP1
NM_030796.5
MANE Select
c.391G>Tp.Gly131Trp
missense
Exon 5 of 5NP_110423.3
VOPP1
NM_001321242.1
c.410G>Tp.Arg137Leu
missense
Exon 5 of 5NP_001308171.1
VOPP1
NM_001321243.2
c.317G>Tp.Arg106Leu
missense
Exon 6 of 6NP_001308172.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
VOPP1
ENST00000285279.10
TSL:1 MANE Select
c.391G>Tp.Gly131Trp
missense
Exon 5 of 5ENSP00000285279.5Q96AW1-1
VOPP1
ENST00000418904.5
TSL:1
c.340G>Tp.Gly114Trp
missense
Exon 5 of 5ENSP00000393210.1Q96AW1-4
VOPP1
ENST00000922470.1
c.388G>Tp.Gly130Trp
missense
Exon 5 of 5ENSP00000592529.1

Frequencies

GnomAD3 genomes
Cov.:
20
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1440568
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
716468
African (AFR)
AF:
0.00
AC:
0
AN:
32396
American (AMR)
AF:
0.00
AC:
0
AN:
39368
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25444
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37994
South Asian (SAS)
AF:
0.00
AC:
0
AN:
82896
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53120
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5696
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1104094
Other (OTH)
AF:
0.00
AC:
0
AN:
59560
GnomAD4 genome
Cov.:
20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Uncertain
0.026
T
BayesDel_noAF
Benign
-0.20
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.026
T
Eigen
Benign
-0.0064
Eigen_PC
Benign
-0.12
FATHMM_MKL
Benign
0.55
D
LIST_S2
Uncertain
0.92
D
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.18
T
MetaSVM
Benign
-0.69
T
MutationAssessor
Benign
0.90
L
PhyloP100
1.9
PrimateAI
Uncertain
0.61
T
PROVEAN
Benign
-1.8
N
REVEL
Benign
0.14
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.0060
D
Polyphen
1.0
D
Vest4
0.51
MutPred
0.29
Gain of catalytic residue at M134 (P = 0.0078)
MVP
0.18
MPC
0.85
ClinPred
0.81
D
GERP RS
3.3
Varity_R
0.12
gMVP
0.69
Mutation Taster
=80/20
polymorphism

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

Other links and lift over

dbSNP: rs769779958; hg19: chr7-55540676; API