rs1188998710
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004209.6(SYNGR3):c.18C>A(p.Phe6Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SYNGR3
NM_004209.6 missense
NM_004209.6 missense
Scores
2
5
11
Clinical Significance
Conservation
PhyloP100: -0.507
Publications
0 publications found
Genes affected
SYNGR3 (HGNC:11501): (synaptogyrin 3) This gene encodes an integral membrane protein. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it is a synaptic vesicle protein that also interacts with the dopamine transporter. The gene product belongs to the synaptogyrin gene family. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.20993376).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004209.6. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SYNGR3 | TSL:1 MANE Select | c.18C>A | p.Phe6Leu | missense | Exon 1 of 4 | ENSP00000248121.2 | O43761 | ||
| SYNGR3 | c.18C>A | p.Phe6Leu | missense | Exon 1 of 4 | ENSP00000543215.1 | ||||
| SYNGR3 | TSL:2 | c.31+289C>A | intron | N/A | ENSP00000455344.1 | H3BPJ5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD2 exomes AF: 0.00 AC: 0AN: 602 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
602
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1066828Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 503970
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1066828
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
503970
African (AFR)
AF:
AC:
0
AN:
22310
American (AMR)
AF:
AC:
0
AN:
7914
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13678
East Asian (EAS)
AF:
AC:
0
AN:
25430
South Asian (SAS)
AF:
AC:
0
AN:
19862
European-Finnish (FIN)
AF:
AC:
0
AN:
20934
Middle Eastern (MID)
AF:
AC:
0
AN:
2868
European-Non Finnish (NFE)
AF:
AC:
0
AN:
911266
Other (OTH)
AF:
AC:
0
AN:
42566
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
MutPred
Loss of loop (P = 0.0804)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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