rs746694647
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_001271.4(CHD2):βc.4231_4233delβ(p.Lys1411del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0000401 in 1,595,054 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (β β ).
Frequency
Genomes: π 0.000026 ( 0 hom., cov: 32)
Exomes π: 0.000042 ( 1 hom. )
Consequence
CHD2
NM_001271.4 inframe_deletion
NM_001271.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.43
Genes affected
CHD2 (HGNC:1917): (chromodomain helicase DNA binding protein 2) The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
Variant 15-93002269-CAAA-C is Benign according to our data. Variant chr15-93002269-CAAA-C is described in ClinVar as [Likely_benign]. Clinvar id is 238882.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAdExome4 at 60 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.4231_4233del | p.Lys1411del | inframe_deletion | 33/39 | ENST00000394196.9 | NP_001262.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.4231_4233del | p.Lys1411del | inframe_deletion | 33/39 | 5 | NM_001271.4 | ENSP00000377747 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151614Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000205 AC: 48AN: 233952Hom.: 0 AF XY: 0.000158 AC XY: 20AN XY: 126938
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GnomAD4 exome AF: 0.0000416 AC: 60AN: 1443440Hom.: 1 AF XY: 0.0000334 AC XY: 24AN XY: 718182
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GnomAD4 genome AF: 0.0000264 AC: 4AN: 151614Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 73982
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2017 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 2020 | - - |
CHD2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 11, 2021 | 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). - |
Developmental and epileptic encephalopathy 94 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at