rs201604061
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP6BS1BS2
The NM_001170629.2(CHD8):c.5402G>A(p.Arg1801His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000548 in 1,597,362 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00037 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00057 ( 0 hom. )
Consequence
CHD8
NM_001170629.2 missense
NM_001170629.2 missense
Scores
13
2
1
Clinical Significance
Conservation
PhyloP100: 7.91
Genes affected
CHD8 (HGNC:20153): (chromodomain helicase DNA binding protein 8) This gene encodes a member of the chromodomain-helicase-DNA binding protein family, which is characterized by a SNF2-like domain and two chromatin organization modifier domains. The encoded protein also contains brahma and kismet domains, which are common to the subfamily of chromodomain-helicase-DNA binding proteins to which this protein belongs. This gene has been shown to function in several processes that include transcriptional regulation, epigenetic remodeling, promotion of cell proliferation, and regulation of RNA synthesis. Allelic variants of this gene are associated with autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, CHD8
BP6
?
Variant 14-21394474-C-T is Benign according to our data. Variant chr14-21394474-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 289377.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Likely_benign=4, Uncertain_significance=2}.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000368 (56/152240) while in subpopulation AMR AF= 0.000654 (10/15290). AF 95% confidence interval is 0.000431. There are 0 homozygotes in gnomad4. There are 27 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 56 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD8 | NM_001170629.2 | c.5402G>A | p.Arg1801His | missense_variant | 31/38 | ENST00000646647.2 | |
CHD8 | NM_020920.4 | c.4565G>A | p.Arg1522His | missense_variant | 31/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD8 | ENST00000646647.2 | c.5402G>A | p.Arg1801His | missense_variant | 31/38 | NM_001170629.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000368 AC: 56AN: 152122Hom.: 0 Cov.: 31
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000312 AC: 68AN: 217978Hom.: 0 AF XY: 0.000263 AC XY: 31AN XY: 117724
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GnomAD4 exome AF: 0.000567 AC: 820AN: 1445122Hom.: 0 Cov.: 34 AF XY: 0.000588 AC XY: 422AN XY: 717528
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GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152240Hom.: 0 Cov.: 31 AF XY: 0.000363 AC XY: 27AN XY: 74460
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 16, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 26, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | CHD8: PP2, PP3, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Intellectual developmental disorder with autism and macrocephaly Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
CHD8-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 28, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;.;.;D;.;.
REVEL
Pathogenic
Sift
Pathogenic
D;D;.;.;D;.;.
Sift4G
Pathogenic
D;D;.;.;D;.;.
Polyphen
D;.;.;D;.;.;.
Vest4
MVP
MPC
1.1
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at