X-75421980-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_144969.3(ZDHHC15):c.747C>T(p.Cys249=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000874 in 1,206,364 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 343 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00044 ( 0 hom., 10 hem., cov: 22)
Exomes 𝑓: 0.00092 ( 0 hom. 333 hem. )
Consequence
ZDHHC15
NM_144969.3 synonymous
NM_144969.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.106
Genes affected
ZDHHC15 (HGNC:20342): (zinc finger DHHC-type palmitoyltransferase 15) The protein encoded by this gene belongs to the DHHC palmitoyltransferase family. Mutations in this gene are associated with mental retardatio X-linked type 91 (MRX91). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant X-75421980-G-A is Benign according to our data. Variant chrX-75421980-G-A is described in ClinVar as [Benign]. Clinvar id is 199186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.106 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 10 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZDHHC15 | NM_144969.3 | c.747C>T | p.Cys249= | synonymous_variant | 9/12 | ENST00000373367.8 | NP_659406.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZDHHC15 | ENST00000373367.8 | c.747C>T | p.Cys249= | synonymous_variant | 9/12 | 1 | NM_144969.3 | ENSP00000362465 | P1 | |
ZDHHC15 | ENST00000541184.1 | c.720C>T | p.Cys240= | synonymous_variant | 8/11 | 2 | ENSP00000445420 |
Frequencies
GnomAD3 genomes AF: 0.000439 AC: 49AN: 111733Hom.: 0 Cov.: 22 AF XY: 0.000295 AC XY: 10AN XY: 33915
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GnomAD3 exomes AF: 0.000537 AC: 96AN: 178820Hom.: 0 AF XY: 0.000581 AC XY: 37AN XY: 63654
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GnomAD4 exome AF: 0.000918 AC: 1005AN: 1094631Hom.: 0 Cov.: 30 AF XY: 0.000924 AC XY: 333AN XY: 360539
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GnomAD4 genome AF: 0.000439 AC: 49AN: 111733Hom.: 0 Cov.: 22 AF XY: 0.000295 AC XY: 10AN XY: 33915
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 05, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 06, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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