rs780977518
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001271.4(CHD2):c.4278+7_4278+9dup variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000176 in 1,591,734 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
CHD2
NM_001271.4 splice_donor_region, intron
NM_001271.4 splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.267
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 15-93002320-A-AATG is Benign according to our data. Variant chr15-93002320-A-AATG is described in ClinVar as [Likely_benign]. Clinvar id is 541369.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAdExome4 at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD2 | NM_001271.4 | c.4278+7_4278+9dup | splice_donor_region_variant, intron_variant | ENST00000394196.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD2 | ENST00000394196.9 | c.4278+7_4278+9dup | splice_donor_region_variant, intron_variant | 5 | NM_001271.4 | P1 | |||
CHD2 | ENST00000626874.2 | c.4278+7_4278+9dup | splice_donor_region_variant, intron_variant | 1 | |||||
CHD2 | ENST00000625662.3 | c.*449+7_*449+9dup | splice_donor_region_variant, intron_variant, NMD_transcript_variant | 5 | |||||
CHD2 | ENST00000629104.1 | c.*511+7_*511+9dup | splice_donor_region_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000355 AC: 8AN: 225090Hom.: 0 AF XY: 0.0000328 AC XY: 4AN XY: 122092
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GnomAD4 exome AF: 0.0000167 AC: 24AN: 1439396Hom.: 0 Cov.: 31 AF XY: 0.0000210 AC XY: 15AN XY: 715638
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74510
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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 | Sep 20, 2023 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at