22-50246704-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_032019.6(HDAC10):c.1546C>A(p.Arg516Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,459,530 control chromosomes in the GnomAD database, including 1 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: not found (cov: 33)
Exomes 𝑓: 0.000027 ( 1 hom. )
Consequence
HDAC10
NM_032019.6 synonymous
NM_032019.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.156
Publications
0 publications found
Genes affected
HDAC10 (HGNC:18128): (histone deacetylase 10) The protein encoded by this gene belongs to the histone deacetylase family, members of which deacetylate lysine residues on the N-terminal part of the core histones. Histone deacetylation modulates chromatin structure, and plays an important role in transcriptional regulation, cell cycle progression, and developmental events. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
MAPK12 (HGNC:6874): (mitogen-activated protein kinase 12) Activation of members of the mitogen-activated protein kinase family is a major mechanism for transduction of extracellular signals. Stress-activated protein kinases are one subclass of MAP kinases. The protein encoded by this gene functions as a signal transducer during differentiation of myoblasts to myotubes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP7
Synonymous conserved (PhyloP=0.156 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_032019.6. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HDAC10 | TSL:1 MANE Select | c.1546C>A | p.Arg516Arg | synonymous | Exon 16 of 20 | ENSP00000216271.5 | Q969S8-1 | ||
| HDAC10 | TSL:1 | c.1486C>A | p.Arg496Arg | synonymous | Exon 15 of 19 | ENSP00000343540.4 | Q969S8-2 | ||
| HDAC10 | TSL:1 | n.*1067C>A | non_coding_transcript_exon | Exon 14 of 18 | ENSP00000397517.1 | Q08AP5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00000798 AC: 2AN: 250732 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
250732
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1459530Hom.: 1 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 726066 show subpopulations
GnomAD4 exome
AF:
AC:
39
AN:
1459530
Hom.:
Cov.:
32
AF XY:
AC XY:
15
AN XY:
726066
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33430
American (AMR)
AF:
AC:
0
AN:
44714
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86194
European-Finnish (FIN)
AF:
AC:
0
AN:
52498
Middle Eastern (MID)
AF:
AC:
0
AN:
4722
European-Non Finnish (NFE)
AF:
AC:
37
AN:
1111884
Other (OTH)
AF:
AC:
2
AN:
60256
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.453
Heterozygous variant carriers
0
3
5
8
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13
0.00
0.20
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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8
12
16
20
<30
30-35
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40-45
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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