11-67034699-C-G

Variant summary

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

The NM_177963.4(SYT12):​c.89C>G​(p.Ala30Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000551 in 1,451,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

SYT12
NM_177963.4 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.82
Variant links:
Genes affected
SYT12 (HGNC:18381): (synaptotagmin 12) This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. Studies of the orthologous gene in rat have shown that the encoded protein selectively modulates spontaneous synaptic-vesicle exocytosis and may also be involved in regulating calcium independent secretion in nonneuronal cells. Alternative splicing results in multiple transcript variants. The gene has previously been referred to as synaptotagmin XI but has been renamed synaptotagmin XII to be standard with mouse and rat official nomenclature.[provided by RefSeq, Apr 2010]

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=0.16463307).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SYT12NM_177963.4 linkc.89C>G p.Ala30Gly missense_variant Exon 3 of 8 ENST00000527043.6 NP_808878.1 Q8IV01Q8NDM9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SYT12ENST00000527043.6 linkc.89C>G p.Ala30Gly missense_variant Exon 3 of 8 1 NM_177963.4 ENSP00000435316.1 Q8IV01

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000166
AC:
4
AN:
240624
Hom.:
0
AF XY:
0.0000230
AC XY:
3
AN XY:
130652
show subpopulations
Gnomad AFR exome
AF:
0.00
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:
0.00
Gnomad NFE exome
AF:
0.0000362
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000551
AC:
8
AN:
1451022
Hom.:
0
Cov.:
32
AF XY:
0.00000970
AC XY:
7
AN XY:
721822
show subpopulations
Gnomad4 AFR exome
AF:
0.00
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:
0.00
Gnomad4 NFE exome
AF:
0.00000632
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jan 05, 2022
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.89C>G (p.A30G) alteration is located in exon 3 (coding exon 2) of the SYT12 gene. This alteration results from a C to G substitution at nucleotide position 89, causing the alanine (A) at amino acid position 30 to be replaced by a glycine (G). 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
0.14
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.025
T;T;T;T
Eigen
Benign
-0.052
Eigen_PC
Benign
0.081
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Benign
0.85
.;.;D;T
M_CAP
Benign
0.0064
T
MetaRNN
Benign
0.16
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.90
L;L;L;.
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-1.3
N;N;N;D
REVEL
Benign
0.046
Sift
Uncertain
0.0060
D;D;D;D
Sift4G
Uncertain
0.0080
D;D;D;D
Polyphen
0.42
B;B;B;.
Vest4
0.37
MVP
0.17
MPC
0.27
ClinPred
0.35
T
GERP RS
4.0
Varity_R
0.17
gMVP
0.52

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: rs776720650; hg19: chr11-66802170; API