chr7-18611791-A-G

Variant names:

• chr7-18611791-A-G
• rs10486292
• NM_178425.4:c.665-17559A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178425.4(HDAC9):​c.665-17559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,160 control chromosomes in the GnomAD database, including 1,350 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 0.12 (1350 hom., cov: 32)
• Consequence: HDAC9 NM_178425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 1 publications found

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]

HDAC9 Gene-Disease associations (from GenCC):

• auriculocondylar syndrome 4

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178425.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDAC9	NM_178425.4	MANE Select	c.665-17559A>G		intron	N/A	NP_848512.1
	HDAC9	NM_178423.3		c.656-17559A>G		intron	N/A	NP_848510.1
	HDAC9	NM_001321868.2		c.721+17762A>G		intron	N/A	NP_001308797.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDAC9	ENST00000686413.1	MANE Select	c.665-17559A>G		intron	N/A	ENSP00000509161.1
	HDAC9	ENST00000441542.7	TSL:1	c.665-17559A>G		intron	N/A	ENSP00000408617.2
	HDAC9	ENST00000406451.8	TSL:1	c.656-17559A>G		intron	N/A	ENSP00000384657.3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17881 AN: 152042 Hom.: 1351 Cov.: 32

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0832

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.112

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.118 AC: 17889 AN: 152160 Hom.: 1350 Cov.: 32 AF XY: 0.120 AC XY: 8932 AN XY: 74398

African (AFR) AF: 0.0749 AC: 3110 AN: 41546

American (AMR) AF: 0.205 AC: 3129 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1793 AN: 5168

South Asian (SAS) AF: 0.173 AC: 835 AN: 4828

European-Finnish (FIN) AF: 0.0832 AC: 882 AN: 10606

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.112 AC: 7597 AN: 67950

Other (OTH) AF: 0.113 AC: 239 AN: 2110

Alfa AF: 0.0523 Hom.: 58

Bravo AF: 0.125

Asia WGS AF: 0.225 AC: 778 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.50
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10486292; hg19: chr7-18651414;