chr15-92984389-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001271.4(CHD2):c.3126C>T(p.Asp1042=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 1,608,960 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0035 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0041 ( 19 hom. )
Consequence
CHD2
NM_001271.4 synonymous
NM_001271.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0780
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 15-92984389-C-T is Benign according to our data. Variant chr15-92984389-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 238879.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-92984389-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.078 with no splicing effect.
BS2
High AC in GnomAd4 at 535 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.3126C>T | p.Asp1042= | synonymous_variant | 25/39 | ENST00000394196.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.3126C>T | p.Asp1042= | synonymous_variant | 25/39 | 5 | NM_001271.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00352 AC: 535AN: 151860Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00411 AC: 1017AN: 247564Hom.: 3 AF XY: 0.00439 AC XY: 588AN XY: 133852
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GnomAD4 exome AF: 0.00407 AC: 5926AN: 1456984Hom.: 19 Cov.: 31 AF XY: 0.00420 AC XY: 3047AN XY: 724774
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GnomAD4 genome AF: 0.00352 AC: 535AN: 151976Hom.: 1 Cov.: 32 AF XY: 0.00372 AC XY: 276AN XY: 74282
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 02, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 29, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | CHD2: BP4, BP7, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 02, 2018 | - - |
Developmental and epileptic encephalopathy 94 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 23, 2022 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2016 | 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. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at