chr6-157382110-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_024630.3(ZDHHC14):c.89A>G(p.Lys30Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000849 in 1,613,032 control chromosomes in the GnomAD database, including 2 homozygotes. 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: 𝑓 0.000059 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000088 ( 2 hom. )
Consequence
ZDHHC14
NM_024630.3 missense
NM_024630.3 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 5.58
Genes affected
ZDHHC14 (HGNC:20341): (zinc finger DHHC-type palmitoyltransferase 14) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010225564).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC14 | NM_024630.3 | c.89A>G | p.Lys30Arg | missense_variant | 1/9 | ENST00000359775.10 | |
ZDHHC14 | NM_153746.2 | c.89A>G | p.Lys30Arg | missense_variant | 1/9 | ||
ZDHHC14 | XM_047419366.1 | c.89A>G | p.Lys30Arg | missense_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC14 | ENST00000359775.10 | c.89A>G | p.Lys30Arg | missense_variant | 1/9 | 1 | NM_024630.3 | A1 | |
ZDHHC14 | ENST00000414563.6 | c.89A>G | p.Lys30Arg | missense_variant | 1/9 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151862Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000189 AC: 47AN: 248962Hom.: 0 AF XY: 0.000252 AC XY: 34AN XY: 134768
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GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461052Hom.: 2 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 726774
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GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 151980Hom.: 0 Cov.: 31 AF XY: 0.0000942 AC XY: 7AN XY: 74308
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.89A>G (p.K30R) alteration is located in exon 1 (coding exon 1) of the ZDHHC14 gene. This alteration results from a A to G substitution at nucleotide position 89, causing the lysine (K) at amino acid position 30 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Loss of methylation at K30 (P = 0.0111);Loss of methylation at K30 (P = 0.0111);
MVP
MPC
0.84
ClinPred
T
GERP RS
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