chr14-21385470-AT-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001170629.2(CHD8):c.*142del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 138,474 control chromosomes in the GnomAD database, including 417 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.047 ( 417 hom., cov: 31)
Exomes 𝑓: 0.28 ( 25 hom. )
Failed GnomAD Quality Control
Consequence
CHD8
NM_001170629.2 3_prime_UTR
NM_001170629.2 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.06
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 -10 ACMG points.
BP6
?
Variant 14-21385470-AT-A is Benign according to our data. Variant chr14-21385470-AT-A is described in ClinVar as [Benign]. Clinvar id is 1183346.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD8 | NM_001170629.2 | c.*142del | 3_prime_UTR_variant | 38/38 | ENST00000646647.2 | ||
LOC107984643 | XR_001750627.2 | n.441+772del | intron_variant, non_coding_transcript_variant | ||||
CHD8 | NM_020920.4 | c.*142del | 3_prime_UTR_variant | 38/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD8 | ENST00000646647.2 | c.*142del | 3_prime_UTR_variant | 38/38 | NM_001170629.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0471 AC: 6517AN: 138444Hom.: 415 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.281 AC: 237779AN: 845428Hom.: 25 Cov.: 0 AF XY: 0.283 AC XY: 116926AN XY: 412990
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Data not reliable, filtered out with message: InbreedingCoeff
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GnomAD4 genome ? AF: 0.0472 AC: 6536AN: 138474Hom.: 417 Cov.: 31 AF XY: 0.0470 AC XY: 3148AN XY: 66910
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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 submitter | clinical testing | GeneDx | Aug 20, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at