rs10236525

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001321868.2(HDAC9):​c.26-124213T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,112 control chromosomes in the GnomAD database, including 3,586 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 0.21 ( 3586 hom., cov: 32)

Consequence

HDAC9
NM_001321868.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0590
Variant links:
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=-0.86).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HDAC9NM_001204144.3 linkuse as main transcriptc.26-86793T>C intron_variant
HDAC9NM_001321868.2 linkuse as main transcriptc.26-124213T>C intron_variant
HDAC9NM_001321869.2 linkuse as main transcriptc.26-124213T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HDAC9ENST00000413509.6 linkuse as main transcriptc.-42+81534T>C intron_variant 5
HDAC9ENST00000417496.6 linkuse as main transcriptc.26-86793T>C intron_variant 2 Q9UKV0-8
HDAC9ENST00000433709.6 linkuse as main transcriptc.-110-23066T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.212
AC:
32220
AN:
151994
Hom.:
3586
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.178
Gnomad AMI
AF:
0.173
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.183
Gnomad EAS
AF:
0.209
Gnomad SAS
AF:
0.151
Gnomad FIN
AF:
0.259
Gnomad MID
AF:
0.119
Gnomad NFE
AF:
0.228
Gnomad OTH
AF:
0.205
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.212
AC:
32227
AN:
152112
Hom.:
3586
Cov.:
32
AF XY:
0.211
AC XY:
15683
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.178
Gnomad4 AMR
AF:
0.233
Gnomad4 ASJ
AF:
0.183
Gnomad4 EAS
AF:
0.209
Gnomad4 SAS
AF:
0.150
Gnomad4 FIN
AF:
0.259
Gnomad4 NFE
AF:
0.228
Gnomad4 OTH
AF:
0.204
Alfa
AF:
0.221
Hom.:
6340
Bravo
AF:
0.208
Asia WGS
AF:
0.231
AC:
801
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.0
DANN
Benign
0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10236525; hg19: chr7-18411672; API