rs12155400

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.118
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]

Genome browser will be placed here

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
HDAC9NM_001204144.3 linkuse as main transcriptc.26-69544A>G intron_variant NP_001191073.1
HDAC9NM_001321868.2 linkuse as main transcriptc.26-106964A>G intron_variant NP_001308797.1
HDAC9NM_001321869.2 linkuse as main transcriptc.26-106964A>G intron_variant NP_001308798.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HDAC9ENST00000413509.6 linkuse as main transcriptc.-42+98783A>G intron_variant 5 ENSP00000412497
HDAC9ENST00000417496.6 linkuse as main transcriptc.26-69544A>G intron_variant 2 ENSP00000401669 Q9UKV0-8
HDAC9ENST00000433709.6 linkuse as main transcriptc.-110-5817A>G intron_variant 3 ENSP00000409003

Frequencies

GnomAD3 genomes
AF:
0.0294
AC:
4467
AN:
152180
Hom.:
95
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00825
Gnomad AMI
AF:
0.0121
Gnomad AMR
AF:
0.0457
Gnomad ASJ
AF:
0.0233
Gnomad EAS
AF:
0.00154
Gnomad SAS
AF:
0.0513
Gnomad FIN
AF:
0.0591
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0352
Gnomad OTH
AF:
0.0249
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0294
AC:
4470
AN:
152298
Hom.:
95
Cov.:
31
AF XY:
0.0301
AC XY:
2239
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.00823
Gnomad4 AMR
AF:
0.0459
Gnomad4 ASJ
AF:
0.0233
Gnomad4 EAS
AF:
0.00154
Gnomad4 SAS
AF:
0.0514
Gnomad4 FIN
AF:
0.0591
Gnomad4 NFE
AF:
0.0352
Gnomad4 OTH
AF:
0.0246
Alfa
AF:
0.0315
Hom.:
13
Bravo
AF:
0.0286
Asia WGS
AF:
0.0190
AC:
66
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.5
DANN
Benign
0.59

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: rs12155400; hg19: chr7-18428921; API