chr14-21385769-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001170629.2(CHD8):c.7590G>A(p.Arg2530=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000239 in 1,550,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
CHD8
NM_001170629.2 synonymous
NM_001170629.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.48
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 14-21385769-C-T is Benign according to our data. Variant chr14-21385769-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1919602.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.48 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD8 | NM_001170629.2 | c.7590G>A | p.Arg2530= | synonymous_variant | 38/38 | ENST00000646647.2 | |
LOC107984643 | XR_001750627.2 | n.441+1056C>T | intron_variant, non_coding_transcript_variant | ||||
CHD8 | NM_020920.4 | c.6753G>A | p.Arg2251= | synonymous_variant | 38/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD8 | ENST00000646647.2 | c.7590G>A | p.Arg2530= | synonymous_variant | 38/38 | NM_001170629.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000265 AC: 4AN: 151182Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000191 AC: 3AN: 156814Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82868
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GnomAD4 exome AF: 0.0000236 AC: 33AN: 1399504Hom.: 0 Cov.: 35 AF XY: 0.0000203 AC XY: 14AN XY: 690254
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 25, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at