15-92901264-AGAG-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4_SupportingPP3
The NM_001271.4(CHD2):c.33_35del(p.Glu11del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,606,488 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. E10E) has been classified as Likely benign.
Frequency
Consequence
NM_001271.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.33_35del | p.Glu11del | inframe_deletion | 2/39 | ENST00000394196.9 | |
CHD2 | NM_001042572.3 | c.33_35del | p.Glu11del | inframe_deletion | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.33_35del | p.Glu11del | inframe_deletion | 2/39 | 5 | NM_001271.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249084Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134636
GnomAD4 exome AF: 0.00000550 AC: 8AN: 1454320Hom.: 0 AF XY: 0.00000414 AC XY: 3AN XY: 723838
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy 94 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2023 | This variant, c.33_35del, results in the deletion of 1 amino acid(s) of the CHD2 protein (p.Glu11del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs772244385, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with CHD2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at