rs17215796
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_178566.6(ZDHHC21):āc.318T>Cā(p.Cys106=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,611,824 control chromosomes in the GnomAD database, including 17,552 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.12 ( 1305 hom., cov: 32)
Exomes š: 0.14 ( 16247 hom. )
Consequence
ZDHHC21
NM_178566.6 synonymous
NM_178566.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.54
Genes affected
ZDHHC21 (HGNC:20750): (zinc finger DHHC-type palmitoyltransferase 21) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP7
?
Synonymous conserved (PhyloP=1.54 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC21 | NM_178566.6 | c.318T>C | p.Cys106= | synonymous_variant | 6/10 | ENST00000380916.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC21 | ENST00000380916.9 | c.318T>C | p.Cys106= | synonymous_variant | 6/10 | 1 | NM_178566.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.118 AC: 17928AN: 152158Hom.: 1307 Cov.: 32
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GnomAD3 exomes AF: 0.126 AC: 31544AN: 250046Hom.: 2357 AF XY: 0.124 AC XY: 16817AN XY: 135194
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GnomAD4 exome AF: 0.144 AC: 209559AN: 1459548Hom.: 16247 Cov.: 31 AF XY: 0.141 AC XY: 102532AN XY: 726080
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GnomAD4 genome ? AF: 0.118 AC: 17925AN: 152276Hom.: 1305 Cov.: 32 AF XY: 0.114 AC XY: 8526AN XY: 74464
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at