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GeneBe

6-113946123-T-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001527.4(HDAC2):c.867A>T(p.Val289=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000505 in 1,613,470 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00041 ( 1 hom. )

Consequence

HDAC2
NM_001527.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0460
Variant links:
Genes affected
HDAC2 (HGNC:4853): (histone deacetylase 2) This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. Thus, it plays an important role in transcriptional regulation, cell cycle progression and developmental events. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 6-113946123-T-A is Benign according to our data. Variant chr6-113946123-T-A is described in ClinVar as [Benign]. Clinvar id is 782745.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.046 with no splicing effect.
BS2
High AC in GnomAd at 219 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HDAC2NM_001527.4 linkuse as main transcriptc.867A>T p.Val289= synonymous_variant 9/14 ENST00000519065.6
HDAC2XM_047418692.1 linkuse as main transcriptc.777A>T p.Val259= synonymous_variant 9/14
HDAC2NR_033441.2 linkuse as main transcriptn.1135A>T non_coding_transcript_exon_variant 10/15
HDAC2NR_073443.2 linkuse as main transcriptn.1065A>T non_coding_transcript_exon_variant 9/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HDAC2ENST00000519065.6 linkuse as main transcriptc.867A>T p.Val289= synonymous_variant 9/141 NM_001527.4 P1Q92769-1

Frequencies

GnomAD3 genomes
AF:
0.00144
AC:
219
AN:
152212
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00446
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000785
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000783
AC:
195
AN:
249164
Hom.:
1
AF XY:
0.000614
AC XY:
83
AN XY:
135202
show subpopulations
Gnomad AFR exome
AF:
0.00414
Gnomad AMR exome
AF:
0.00139
Gnomad ASJ exome
AF:
0.00378
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000319
Gnomad OTH exome
AF:
0.00132
GnomAD4 exome
AF:
0.000407
AC:
595
AN:
1461140
Hom.:
1
Cov.:
29
AF XY:
0.000351
AC XY:
255
AN XY:
726894
show subpopulations
Gnomad4 AFR exome
AF:
0.00520
Gnomad4 AMR exome
AF:
0.00127
Gnomad4 ASJ exome
AF:
0.00383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000156
Gnomad4 OTH exome
AF:
0.00123
GnomAD4 genome
AF:
0.00144
AC:
220
AN:
152330
Hom.:
0
Cov.:
33
AF XY:
0.00132
AC XY:
98
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.00447
Gnomad4 AMR
AF:
0.000784
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000826
Hom.:
0
Bravo
AF:
0.00174
EpiCase
AF:
0.000491
EpiControl
AF:
0.000178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 24, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.36
Cadd
Benign
5.1
Dann
Benign
0.76

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: rs77438668; hg19: chr6-114267287; API