3-13498834-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024827.4(HDAC11):c.412+279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,132 control chromosomes in the GnomAD database, including 61,389 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 0.90 ( 61389 hom., cov: 30)
Consequence
HDAC11
NM_024827.4 intron
NM_024827.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.159
Genes affected
HDAC11 (HGNC:19086): (histone deacetylase 11) This gene encodes a class IV histone deacetylase. The encoded protein is localized to the nucleus and may be involved in regulating the expression of interleukin 10. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Apr 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC11 | NM_024827.4 | c.412+279G>A | intron_variant | ENST00000295757.8 | NP_079103.2 | |||
HDAC11 | NM_001136041.3 | c.259+279G>A | intron_variant | NP_001129513.1 | ||||
HDAC11 | NM_001330636.2 | c.253-3037G>A | intron_variant | NP_001317565.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC11 | ENST00000295757.8 | c.412+279G>A | intron_variant | 1 | NM_024827.4 | ENSP00000295757.3 |
Frequencies
GnomAD3 genomes AF: 0.897 AC: 136376AN: 152014Hom.: 61326 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.897 AC: 136498AN: 152132Hom.: 61389 Cov.: 30 AF XY: 0.899 AC XY: 66873AN XY: 74376
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ClinVar
Not reported inComputational scores
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Name
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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