NM_178425.4:c.2803+12364C>T

Variant names:

• chr7-18886960-C-T
• rs11768780
• NM_178425.4:c.2803+12364C>T

Variant summary

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

The NM_178425.4(HDAC9):​c.2803+12364C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,014 control chromosomes in the GnomAD database, including 3,753 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 (3753 hom., cov: 33)
• Consequence: HDAC9 NM_178425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 4 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-AS1 (HGNC:40664): (HDAC9 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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.2803+12364C>T		intron	N/A	NP_848512.1
	HDAC9	NM_178423.3		c.2794+12364C>T		intron	N/A	NP_848510.1
	HDAC9	NM_001321868.2		c.2728+12364C>T		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.2803+12364C>T		intron	N/A	ENSP00000509161.1
	HDAC9	ENST00000441542.7	TSL:1	c.2803+12364C>T		intron	N/A	ENSP00000408617.2
	HDAC9	ENST00000406451.8	TSL:1	c.2794+12364C>T		intron	N/A	ENSP00000384657.3

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32533 AN: 151896 Hom.: 3751 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.214 AC: 32549 AN: 152014 Hom.: 3753 Cov.: 33 AF XY: 0.221 AC XY: 16418 AN XY: 74316

African (AFR) AF: 0.119 AC: 4922 AN: 41454

American (AMR) AF: 0.260 AC: 3969 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 821 AN: 3472

East Asian (EAS) AF: 0.158 AC: 816 AN: 5180

South Asian (SAS) AF: 0.333 AC: 1606 AN: 4822

European-Finnish (FIN) AF: 0.317 AC: 3345 AN: 10542

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16383 AN: 67956

Other (OTH) AF: 0.208 AC: 437 AN: 2106

Alfa AF: 0.139 Hom.: 363

Bravo AF: 0.204

Asia WGS AF: 0.260 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-1.7
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: rs11768780; hg19: chr7-18926583;