rs12155400
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001321868.2(HDAC9):c.26-106964A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 152,298 control chromosomes in the GnomAD database, including 95 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 0.029 ( 95 hom., cov: 31)
Consequence
HDAC9
NM_001321868.2 intron
NM_001321868.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.118
Genes affected
HDAC9 (HGNC:14065): (histone deacetylase 9) 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 has sequence homology to members of the histone deacetylase family. This gene is orthologous to the Xenopus and mouse MITR genes. The MITR protein lacks the histone deacetylase catalytic domain. It represses MEF2 activity through recruitment of multicomponent corepressor complexes that include CtBP and HDACs. This encoded protein may play a role in hematopoiesis. Multiple alternatively spliced transcripts have been described for this gene but the full-length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]
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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=-0.88).
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0294 (4470/152298) while in subpopulation SAS AF= 0.0514 (248/4828). AF 95% confidence interval is 0.0461. There are 95 homozygotes in gnomad4. There are 2239 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 4470 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC9 | NM_001204144.3 | c.26-69544A>G | intron_variant | NP_001191073.1 | ||||
HDAC9 | NM_001321868.2 | c.26-106964A>G | intron_variant | NP_001308797.1 | ||||
HDAC9 | NM_001321869.2 | c.26-106964A>G | intron_variant | NP_001308798.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC9 | ENST00000413509.6 | c.-42+98783A>G | intron_variant | 5 | ENSP00000412497 | |||||
HDAC9 | ENST00000417496.6 | c.26-69544A>G | intron_variant | 2 | ENSP00000401669 | |||||
HDAC9 | ENST00000433709.6 | c.-110-5817A>G | intron_variant | 3 | ENSP00000409003 |
Frequencies
GnomAD3 genomes AF: 0.0294 AC: 4467AN: 152180Hom.: 95 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0294 AC: 4470AN: 152298Hom.: 95 Cov.: 31 AF XY: 0.0301 AC XY: 2239AN XY: 74476
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66
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at