chrX-72330084-CAG-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_018486.3(HDAC8):c.1112-10_1112-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,201,722 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000089 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.0000018 ( 0 hom. 1 hem. )
Consequence
HDAC8
NM_018486.3 splice_polypyrimidine_tract, intron
NM_018486.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.15
Genes affected
HDAC8 (HGNC:13315): (histone deacetylase 8) Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to class I of the histone deacetylase family. It catalyzes the deacetylation of lysine residues in the histone N-terminal tails and represses transcription in large multiprotein complexes with transcriptional co-repressors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant X-72330084-CAG-C is Benign according to our data. Variant chrX-72330084-CAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2026394.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDAC8 | NM_018486.3 | c.1112-10_1112-9del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000373573.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDAC8 | ENST00000373573.9 | c.1112-10_1112-9del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018486.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 112008Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34178
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GnomAD4 exome AF: 0.00000184 AC: 2AN: 1089714Hom.: 0 AF XY: 0.00000281 AC XY: 1AN XY: 355358
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GnomAD4 genome AF: 0.00000893 AC: 1AN: 112008Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34178
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cornelia de Lange syndrome 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 23, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at