1-27812258-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_177424.3(STX12):c.566G>A(p.Arg189Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000103 in 1,555,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
STX12
NM_177424.3 missense
NM_177424.3 missense
Scores
5
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.08
Genes affected
STX12 (HGNC:11430): (syntaxin 12) Predicted to enable SNAP receptor activity and SNARE binding activity. Involved in autophagosome assembly; cholesterol efflux; and protein stabilization. Located in several cellular components, including membrane raft; phagocytic vesicle; and phagophore assembly site. Part of SNARE complex. Colocalizes with BLOC-1 complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.26732022).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX12 | NM_177424.3 | c.566G>A | p.Arg189Gln | missense_variant | 6/9 | ENST00000373943.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX12 | ENST00000373943.9 | c.566G>A | p.Arg189Gln | missense_variant | 6/9 | 1 | NM_177424.3 | P1 | |
STX12 | ENST00000440806.2 | c.635G>A | p.Arg212Gln | missense_variant | 7/7 | 3 | |||
STX12 | ENST00000472285.1 | n.139G>A | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
STX12 | ENST00000481874.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000123 AC: 2AN: 162522Hom.: 0 AF XY: 0.0000234 AC XY: 2AN XY: 85610
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GnomAD4 exome AF: 0.00000998 AC: 14AN: 1403042Hom.: 0 Cov.: 30 AF XY: 0.0000116 AC XY: 8AN XY: 692390
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74304
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;D
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Loss of phosphorylation at T186 (P = 0.1194);.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at