chr17-7885025-CCCGCCG-C
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS1
The NM_001437504.1(CHD3):c.237_242delGCCGCC(p.Pro80_Pro81del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,161,154 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 0.00013 ( 0 hom., cov: 27)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
CHD3
NM_001437504.1 disruptive_inframe_deletion
NM_001437504.1 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.113
Publications
0 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 -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001437504.1
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000133 (19/143280) while in subpopulation EAS AF = 0.00144 (7/4870). AF 95% confidence interval is 0.000675. There are 0 homozygotes in GnomAd4. There are 9 alleles in the male GnomAd4 subpopulation. Median coverage is 27. This position passed quality control check.
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.237_242delGCCGCC | p.Pro80_Pro81del | disruptive_inframe_deletion | Exon 1 of 40 | NP_001424433.1 | A0A8V8TR54 | |||
| CHD3 | c.237_242delGCCGCC | p.Pro80_Pro81del | disruptive_inframe_deletion | Exon 1 of 40 | NP_001005271.2 | Q12873-3 | |||
| CHD3 | c.237_242delGCCGCC | p.Pro80_Pro81del | disruptive_inframe_deletion | Exon 1 of 40 | NP_001424438.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CHD3 | c.237_242delGCCGCC | p.Pro80_Pro81del | disruptive_inframe_deletion | Exon 1 of 40 | ENSP00000515165.1 | A0A8V8TR54 | |||
| CHD3 | TSL:2 | c.237_242delGCCGCC | p.Pro80_Pro81del | disruptive_inframe_deletion | Exon 1 of 40 | ENSP00000369716.4 | Q12873-3 | ||
| NAA38 | TSL:3 | c.-167+134_-167+139delCGGCGG | intron | N/A | ENSP00000461545.1 | I3L4V0 |
Frequencies
GnomAD3 genomes 0.000133 AC: 19AN: 143180Hom.: 0 Cov.: 27 show subpopulations
GnomAD3 genomes
AF:
AC:
19
AN:
143180
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: 0.000100 AC: 102AN: 1017874Hom.: 0 AF XY: 0.000106 AC XY: 51AN XY: 482950 show subpopulations
GnomAD4 exome
AF:
AC:
102
AN:
1017874
Hom.:
AF XY:
AC XY:
51
AN XY:
482950
show subpopulations
African (AFR)
AF:
AC:
12
AN:
20580
American (AMR)
AF:
AC:
0
AN:
7444
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11712
East Asian (EAS)
AF:
AC:
24
AN:
21584
South Asian (SAS)
AF:
AC:
4
AN:
19870
European-Finnish (FIN)
AF:
AC:
0
AN:
17760
Middle Eastern (MID)
AF:
AC:
1
AN:
2606
European-Non Finnish (NFE)
AF:
AC:
52
AN:
877490
Other (OTH)
AF:
AC:
9
AN:
38828
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.454
Heterozygous variant carriers
0
4
8
12
16
20
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.000133 AC: 19AN: 143280Hom.: 0 Cov.: 27 AF XY: 0.000129 AC XY: 9AN XY: 69602 show subpopulations
GnomAD4 genome
AF:
AC:
19
AN:
143280
Hom.:
Cov.:
27
AF XY:
AC XY:
9
AN XY:
69602
show subpopulations
African (AFR)
AF:
AC:
9
AN:
40054
American (AMR)
AF:
AC:
0
AN:
14512
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3374
East Asian (EAS)
AF:
AC:
7
AN:
4870
South Asian (SAS)
AF:
AC:
0
AN:
4712
European-Finnish (FIN)
AF:
AC:
0
AN:
7970
Middle Eastern (MID)
AF:
AC:
0
AN:
266
European-Non Finnish (NFE)
AF:
AC:
3
AN:
64654
Other (OTH)
AF:
AC:
0
AN:
1990
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
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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