3-13498834-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159
Variant links:
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]

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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HDAC11NM_024827.4 linkuse as main transcriptc.412+279G>A intron_variant ENST00000295757.8 NP_079103.2 Q96DB2-1
HDAC11NM_001136041.3 linkuse as main transcriptc.259+279G>A intron_variant NP_001129513.1 Q96DB2-2
HDAC11NM_001330636.2 linkuse as main transcriptc.253-3037G>A intron_variant NP_001317565.1 B5MCQ6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HDAC11ENST00000295757.8 linkuse as main transcriptc.412+279G>A intron_variant 1 NM_024827.4 ENSP00000295757.3 Q96DB2-1

Frequencies

GnomAD3 genomes
AF:
0.897
AC:
136376
AN:
152014
Hom.:
61326
Cov.:
30
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.959
Gnomad4 AMR
AF:
0.906
Gnomad4 ASJ
AF:
0.813
Gnomad4 EAS
AF:
0.907
Gnomad4 SAS
AF:
0.888
Gnomad4 FIN
AF:
0.900
Gnomad4 NFE
AF:
0.861
Gnomad4 OTH
AF:
0.887
Alfa
AF:
0.864
Hom.:
79416
Bravo
AF:
0.900
Asia WGS
AF:
0.890
AC:
3094
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.2
DANN
Benign
0.49

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2675231; hg19: chr3-13540334; API