9-128724048-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032799.5(ZDHHC12):āc.46G>Cā(p.Gly16Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000745 in 1,611,280 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 (ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 32)
Exomes š: 0.0000055 ( 0 hom. )
Consequence
ZDHHC12
NM_032799.5 missense
NM_032799.5 missense
Scores
2
2
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.10
Genes affected
ZDHHC12 (HGNC:19159): (zinc finger DHHC-type palmitoyltransferase 12) Enables palmitoyltransferase activity. Involved in protein palmitoylation. Located in Golgi apparatus and endoplasmic reticulum. [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=0.35028595).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC12 | NM_032799.5 | c.46G>C | p.Gly16Arg | missense_variant | 1/5 | ENST00000372663.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC12 | ENST00000372663.9 | c.46G>C | p.Gly16Arg | missense_variant | 1/5 | 1 | NM_032799.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152094Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000163 AC: 4AN: 245236Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133140
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GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459186Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 725706
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74314
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;.;T
Polyphen
D;.;.;.
Vest4
MutPred
Gain of methylation at G16 (P = 0.0089);Gain of methylation at G16 (P = 0.0089);Gain of methylation at G16 (P = 0.0089);Gain of methylation at G16 (P = 0.0089);
MVP
MPC
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D
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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