rs2306159
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The ENST00000369405.7(ZDHHC6):c.618C>T(p.Thr206=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 1,612,808 control chromosomes in the GnomAD database, including 276,110 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: 𝑓 0.53 ( 21615 hom., cov: 32)
Exomes 𝑓: 0.59 ( 254495 hom. )
Consequence
ZDHHC6
ENST00000369405.7 synonymous
ENST00000369405.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.446
Genes affected
ZDHHC6 (HGNC:19160): (zinc finger DHHC-type palmitoyltransferase 6) Enables palmitoyltransferase activity. Involved in positive regulation of mitochondrial fusion and protein 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 Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP7
Synonymous conserved (PhyloP=0.446 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZDHHC6 | NM_022494.3 | c.618C>T | p.Thr206= | synonymous_variant | 5/11 | ENST00000369405.7 | NP_071939.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZDHHC6 | ENST00000369405.7 | c.618C>T | p.Thr206= | synonymous_variant | 5/11 | 1 | NM_022494.3 | ENSP00000358413 | P4 |
Frequencies
GnomAD3 genomes AF: 0.525 AC: 79783AN: 151826Hom.: 21609 Cov.: 32
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GnomAD3 exomes AF: 0.568 AC: 142750AN: 251104Hom.: 41592 AF XY: 0.569 AC XY: 77284AN XY: 135714
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GnomAD4 exome AF: 0.587 AC: 858062AN: 1460864Hom.: 254495 Cov.: 50 AF XY: 0.588 AC XY: 427596AN XY: 726726
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GnomAD4 genome AF: 0.525 AC: 79838AN: 151944Hom.: 21615 Cov.: 32 AF XY: 0.527 AC XY: 39151AN XY: 74274
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
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