rs150268140
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_ModerateBP6_Very_StrongBS2
The NM_001271.4(CHD2):āc.3126C>Gā(p.Asp1042Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000678 in 1,608,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. D1042D) has been classified as Likely benign.
Frequency
Consequence
NM_001271.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.3126C>G | p.Asp1042Glu | missense_variant | 25/39 | ENST00000394196.9 | NP_001262.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.3126C>G | p.Asp1042Glu | missense_variant | 25/39 | 5 | NM_001271.4 | ENSP00000377747.4 |
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151864Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247564Hom.: 0 AF XY: 0.0000374 AC XY: 5AN XY: 133852
GnomAD4 exome AF: 0.0000659 AC: 96AN: 1456992Hom.: 0 Cov.: 31 AF XY: 0.0000745 AC XY: 54AN XY: 724776
GnomAD4 genome AF: 0.0000856 AC: 13AN: 151864Hom.: 0 Cov.: 32 AF XY: 0.0000944 AC XY: 7AN XY: 74156
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 18, 2020 | - - |
Developmental and epileptic encephalopathy 94 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at