rs1184559933
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 3P and 3B. PM2PP2BP4BP6_Moderate
The NM_001271.4(CHD2):āc.4363C>Gā(p.Pro1455Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
CHD2
NM_001271.4 missense
NM_001271.4 missense
Scores
1
10
4
Clinical Significance
Conservation
PhyloP100: 7.20
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, CHD2
BP4
?
Computational evidence support a benign effect (MetaRNN=0.4041983).
BP6
?
Variant 15-93004701-C-G is Benign according to our data. Variant chr15-93004701-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 474391.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.4363C>G | p.Pro1455Ala | missense_variant | 34/39 | ENST00000394196.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.4363C>G | p.Pro1455Ala | missense_variant | 34/39 | 5 | NM_001271.4 | P1 | |
CHD2 | ENST00000626874.2 | c.4363C>G | p.Pro1455Ala | missense_variant | 34/38 | 1 | |||
CHD2 | ENST00000630813.1 | n.189C>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
CHD2 | ENST00000625662.3 | c.*534C>G | 3_prime_UTR_variant, NMD_transcript_variant | 30/35 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151998Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251142Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135750
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461328Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726976
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151998Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74226
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy 94 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 04, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MutPred
Loss of helix (P = 0.2662);Loss of helix (P = 0.2662);
MVP
MPC
0.83
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at