10-112438345-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_022494.3(ZDHHC6):c.726T>C(p.Ile242=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,353,784 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0076 ( 13 hom., cov: 32)
Exomes 𝑓: 0.00057 ( 11 hom. )
Consequence
ZDHHC6
NM_022494.3 synonymous
NM_022494.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.51
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
Variant 10-112438345-A-G is Benign according to our data. Variant chr10-112438345-A-G is described in ClinVar as [Benign]. Clinvar id is 778473.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.51 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00758 (1155/152312) while in subpopulation AFR AF= 0.0262 (1090/41572). AF 95% confidence interval is 0.0249. There are 13 homozygotes in gnomad4. There are 563 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC6 | NM_022494.3 | c.726T>C | p.Ile242= | synonymous_variant | 6/11 | ENST00000369405.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC6 | ENST00000369405.7 | c.726T>C | p.Ile242= | synonymous_variant | 6/11 | 1 | NM_022494.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00755 AC: 1149AN: 152194Hom.: 13 Cov.: 32
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GnomAD3 exomes AF: 0.00106 AC: 111AN: 104946Hom.: 1 AF XY: 0.000706 AC XY: 40AN XY: 56634
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GnomAD4 exome AF: 0.000568 AC: 682AN: 1201472Hom.: 11 Cov.: 26 AF XY: 0.000495 AC XY: 291AN XY: 587984
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GnomAD4 genome ? AF: 0.00758 AC: 1155AN: 152312Hom.: 13 Cov.: 32 AF XY: 0.00756 AC XY: 563AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2017 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at