chrX-129806478-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016032.4(ZDHHC9):c.987A>C(p.Thr329=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,205,528 control chromosomes in the GnomAD database, including 1 homozygotes. There are 37 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000052 ( 1 hom. 37 hem. )
Consequence
ZDHHC9
NM_016032.4 synonymous
NM_016032.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.277
Genes affected
ZDHHC9 (HGNC:18475): (zinc finger DHHC-type palmitoyltransferase 9) This gene encodes an integral membrane protein that is a member of the zinc finger DHHC domain-containing protein family. The encoded protein forms a complex with golgin subfamily A member 7 and functions as a palmitoyltransferase. This protein specifically palmitoylates HRAS and NRAS. Mutations in this gene are associated with X-linked cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant X-129806478-T-G is Benign according to our data. Variant chrX-129806478-T-G is described in ClinVar as [Benign]. Clinvar id is 2914820.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAdExome at 14 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC9 | NM_016032.4 | c.987A>C | p.Thr329= | synonymous_variant | 11/11 | ENST00000357166.11 | |
ZDHHC9 | NM_001008222.3 | c.987A>C | p.Thr329= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC9 | ENST00000357166.11 | c.987A>C | p.Thr329= | synonymous_variant | 11/11 | 1 | NM_016032.4 | P1 | |
ZDHHC9 | ENST00000371064.7 | c.987A>C | p.Thr329= | synonymous_variant | 10/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111555Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33721
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GnomAD3 exomes AF: 0.000109 AC: 20AN: 183148Hom.: 0 AF XY: 0.000207 AC XY: 14AN XY: 67650
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GnomAD4 exome AF: 0.0000521 AC: 57AN: 1093920Hom.: 1 Cov.: 29 AF XY: 0.000103 AC XY: 37AN XY: 359316
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Syndromic X-linked intellectual disability Raymond type Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 20, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
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