chr15-93024486-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_ModerateBP6_Very_StrongBS2
The NM_001271.4(CHD2):āc.5268G>Cā(p.Gln1756His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000622 in 1,614,170 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q1756L) has been classified as Uncertain significance.
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 | UniProt |
---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.5268G>C | p.Gln1756His | missense_variant | 39/39 | ENST00000394196.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.5268G>C | p.Gln1756His | missense_variant | 39/39 | 5 | NM_001271.4 | P1 | |
CHD2 | ENST00000625662.3 | c.*1439G>C | 3_prime_UTR_variant, NMD_transcript_variant | 35/35 | 5 | ||||
CHD2 | ENST00000627460.1 | c.*400G>C | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000301 AC: 75AN: 249572Hom.: 0 AF XY: 0.000303 AC XY: 41AN XY: 135404
GnomAD4 exome AF: 0.000655 AC: 958AN: 1461894Hom.: 1 Cov.: 31 AF XY: 0.000624 AC XY: 454AN XY: 727248
GnomAD4 genome AF: 0.000302 AC: 46AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 22, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | CHD2: BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 28, 2018 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 05, 2024 | 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. - |
CHD2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 13, 2023 | 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at