17-7884893-CGAGGAGGAG-CGAGGAGGAGGAGGAGGAG
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_001437504.1(CHD3):c.98_106dupAGGAGGAGG(p.Glu33_Glu35dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000625 in 1,280,720 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000072 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0000061 ( 0 hom. )
Consequence
CHD3
NM_001437504.1 disruptive_inframe_insertion
NM_001437504.1 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.28
Publications
2 publications found
Genes affected
CHD3 (HGNC:1918): (chromodomain helicase DNA binding protein 3) This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
NAA38 (HGNC:28212): (N-alpha-acetyltransferase 38, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex. Colocalizes with polysome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001437504.1
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001437504.1. 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 |
|---|---|---|---|---|---|---|---|---|---|
| CHD3 | c.98_106dupAGGAGGAGG | p.Glu33_Glu35dup | disruptive_inframe_insertion | Exon 1 of 40 | NP_001424433.1 | A0A8V8TR54 | |||
| CHD3 | c.98_106dupAGGAGGAGG | p.Glu33_Glu35dup | disruptive_inframe_insertion | Exon 1 of 40 | NP_001005271.2 | Q12873-3 | |||
| CHD3 | c.98_106dupAGGAGGAGG | p.Glu33_Glu35dup | disruptive_inframe_insertion | Exon 1 of 40 | NP_001424438.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CHD3 | c.98_106dupAGGAGGAGG | p.Glu33_Glu35dup | disruptive_inframe_insertion | Exon 1 of 40 | ENSP00000515165.1 | A0A8V8TR54 | |||
| CHD3 | TSL:2 | c.98_106dupAGGAGGAGG | p.Glu33_Glu35dup | disruptive_inframe_insertion | Exon 1 of 40 | ENSP00000369716.4 | Q12873-3 | ||
| NAA38 | TSL:3 | c.-167+263_-167+271dupCTCCTCCTC | intron | N/A | ENSP00000461545.1 | I3L4V0 |
Frequencies
GnomAD3 genomes 0.00000716 AC: 1AN: 139748Hom.: 0 Cov.: 27 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
139748
Hom.:
Cov.:
27
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000614 AC: 7AN: 1140972Hom.: 0 Cov.: 18 AF XY: 0.00000888 AC XY: 5AN XY: 563280 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1140972
Hom.:
Cov.:
18
AF XY:
AC XY:
5
AN XY:
563280
show subpopulations
African (AFR)
AF:
AC:
0
AN:
23140
American (AMR)
AF:
AC:
1
AN:
22684
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17496
East Asian (EAS)
AF:
AC:
0
AN:
23922
South Asian (SAS)
AF:
AC:
0
AN:
58136
European-Finnish (FIN)
AF:
AC:
0
AN:
32812
Middle Eastern (MID)
AF:
AC:
0
AN:
3246
European-Non Finnish (NFE)
AF:
AC:
6
AN:
915038
Other (OTH)
AF:
AC:
0
AN:
44498
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.446
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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50-55
55-60
60-65
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>80
Age
GnomAD4 genome 0.00000716 AC: 1AN: 139748Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 67954 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
139748
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
67954
show subpopulations
African (AFR)
AF:
AC:
1
AN:
37866
American (AMR)
AF:
AC:
0
AN:
14330
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3278
East Asian (EAS)
AF:
AC:
0
AN:
4660
South Asian (SAS)
AF:
AC:
0
AN:
4420
European-Finnish (FIN)
AF:
AC:
0
AN:
8946
Middle Eastern (MID)
AF:
AC:
0
AN:
282
European-Non Finnish (NFE)
AF:
AC:
0
AN:
63240
Other (OTH)
AF:
AC:
0
AN:
1906
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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