3-13498834-G-A

Variant names:

• chr3-13498834-G-A
• rs2675231
• NM_024827.4:c.412+279G>A

Variant summary

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

The NM_024827.4(HDAC11):​c.412+279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,132 control chromosomes in the GnomAD database, including 61,389 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 0.90 (61389 hom., cov: 30)
• Consequence: HDAC11 NM_024827.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 7 publications found

Genes affected

HDAC11 (HGNC:19086): (histone deacetylase 11) This gene encodes a class IV histone deacetylase. The encoded protein is localized to the nucleus and may be involved in regulating the expression of interleukin 10. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Apr 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024827.4. 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
	HDAC11	NM_024827.4	MANE Select	c.412+279G>A		intron	N/A	NP_079103.2
	HDAC11	NM_001136041.3		c.259+279G>A		intron	N/A	NP_001129513.1
	HDAC11	NM_001330636.2		c.253-3037G>A		intron	N/A	NP_001317565.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDAC11	ENST00000295757.8	TSL:1 MANE Select	c.412+279G>A		intron	N/A	ENSP00000295757.3
	HDAC11	ENST00000437379.2	TSL:1	c.328+279G>A		intron	N/A	ENSP00000395188.2
	HDAC11	ENST00000433119.5	TSL:1	c.286-1879G>A		intron	N/A	ENSP00000412514.1

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136376 AN: 152014 Hom.: 61326 Cov.: 30

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.897 AC: 136498 AN: 152132 Hom.: 61389 Cov.: 30 AF XY: 0.899 AC XY: 66873 AN XY: 74376

African (AFR) AF: 0.959 AC: 39791 AN: 41510

American (AMR) AF: 0.906 AC: 13862 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2819 AN: 3466

East Asian (EAS) AF: 0.907 AC: 4687 AN: 5166

South Asian (SAS) AF: 0.888 AC: 4273 AN: 4810

European-Finnish (FIN) AF: 0.900 AC: 9557 AN: 10622

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58530 AN: 67948

Other (OTH) AF: 0.887 AC: 1872 AN: 2110

Alfa AF: 0.867 Hom.: 110418

Bravo AF: 0.900

Asia WGS AF: 0.890 AC: 3094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.49
PhyloP100		0.16
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: rs2675231; hg19: chr3-13540334;