rs141598514

Variant names:

• chr3-13504243-C-G
• rs141598514
• NM_024827.4:c.799C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-13504243-C-G
• chr3-13504243-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_024827.4(HDAC11):​c.799C>G​(p.Arg267Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R267C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: HDAC11 NM_024827.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.25
• Publications: 0 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]

ENSG00000298100 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDAC11	NM_024827.4	MANE Select	c.799C>G	p.Arg267Gly	missense	Exon 9 of 10	NP_079103.2	Q96DB2-1
	HDAC11	NM_001136041.3		c.646C>G	p.Arg216Gly	missense	Exon 9 of 10	NP_001129513.1	Q96DB2-2
	HDAC11	NM_001330636.2		c.562C>G	p.Arg188Gly	missense	Exon 6 of 7	NP_001317565.1	B5MCQ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDAC11	ENST00000295757.8	TSL:1 MANE Select	c.799C>G	p.Arg267Gly	missense	Exon 9 of 10	ENSP00000295757.3	Q96DB2-1
	HDAC11	ENST00000437379.2	TSL:1	c.715C>G	p.Arg239Gly	missense	Exon 8 of 9	ENSP00000395188.2	E7ETT9
	HDAC11	ENST00000433119.5	TSL:1	c.672C>G	p.Thr224Thr	synonymous	Exon 8 of 9	ENSP00000412514.1	Q658J9

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.31
BayesDel_addAF	Uncertain	0.054	T
BayesDel_noAF	Benign	-0.16
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.087	T
Eigen	Uncertain	0.35
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.97	D
M_CAP	Uncertain	0.12	D
MetaRNN	Uncertain	0.63	D
MetaSVM	Benign	-0.38	T
PhyloP100		7.2
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.70	N
REVEL	Uncertain	0.39
Sift4G	Uncertain	0.012	D
Polyphen		0.26	B
Vest4		0.41
MutPred		0.67		Gain of glycosylation at S272 (P = 0.0459)
MVP		0.92
MPC		0.52
ClinPred		0.99	D
GERP RS		5.5
Varity_R		0.47
gMVP		0.85
Mutation Taster		=71/29	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs141598514; hg19: chr3-13545743;