VCV002567607.5 - ClinVar

NM_001005273.3(CHD3):c.1235G>A (p.Arg412Gln)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Uncertain significance(1); Likely benign(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001005273.3(CHD3):c.1235G>A (p.Arg412Gln)

Variation ID: 2567607 Accession: VCV002567607.5

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 17p13.1 17: 7894574 (GRCh38) [ NCBI UCSC ] 17: 7797892 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Jul 8, 2023	Nov 17, 2024	Aug 1, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001005273.3:c.1235G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001005273.1:p.Arg412Gln	missense
NM_001005271.3:c.1412G>A	NP_001005271.2:p.Arg471Gln	missense
NM_005852.4:c.1235G>A	NP_005843.2:p.Arg412Gln	missense
NC_000017.11:g.7894574G>A
NC_000017.10:g.7797892G>A
NG_086982.1:g.927G>A

... more HGVS ... less HGVS

Protein change

R471Q, R412Q

Other names

Canonical SPDI

NC_000017.11:7894573:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
CHD3		-	-	GRCh38 GRCh37	450	545
LOC126862484	-	-	-	GRCh38	-	37

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Inborn genetic diseases	Likely benign (1)	criteria provided, single submitter	May 31, 2023	RCV003311322.2
CHD3-related disorder	Likely benign (1)	no assertion criteria provided	Sep 11, 2023	RCV003966305.2
Snijders Blok-Campeau syndrome	Uncertain significance (1)	criteria provided, single submitter	Aug 1, 2023	RCV004784138.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely benign (May 31, 2023)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV004007966.2 First in ClinVar: Jul 08, 2023 Last updated: May 01, 2024	Comment: 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 … (more) 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. (less)
Uncertain significance (Aug 01, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Snijders Blok-Campeau syndrome (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center Accession: SCV005397478.1 First in ClinVar: Nov 17, 2024 Last updated: Nov 17, 2024	Comment: This sequence variant is a single nucleotide substitution (G>A) at position 1412 of the coding sequence of the CHD3 gene that results in an arginine … (more) This sequence variant is a single nucleotide substitution (G>A) at position 1412 of the coding sequence of the CHD3 gene that results in an arginine to glutamine amino acid change at residue 471 of the CHD3 protein. This residue falls within the zinc finger domain (Uniprot) which plays an important role in CHD3 function. This variant is absent from ClinVar but is present in 16 of 282576 alleles (0.0057%) in the gnomAD population dataset. Multiple bioinformatic tools predict that this arginine to glutamine amino acid change would be neutral, and the Arg471 residue at this position is highly conserved across the mammalian species examined. Studies examining the functiol consequence of this variant have not been performed, to our knowledge. At this time, there is insufficient evidence to determine if this variant is pathogenic or benign. Therefore, we consider this a variant of uncertain significance. ACMG Criteria: BP4 (less)
Likely benign (Sep 11, 2023)	no assertion criteria provided Method: clinical testing	CHD3-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004781607.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: 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).

Comment:

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.

Comment:

This sequence variant is a single nucleotide substitution (G>A) at position 1412 of the coding sequence of the CHD3 gene that results in an arginine to glutamine amino acid change at residue 471 of the CHD3 protein. This residue falls within the zinc finger domain (Uniprot) which plays an important role in CHD3 function. This variant is absent from ClinVar but is present in 16 of 282576 alleles (0.0057%) in the gnomAD population dataset. Multiple bioinformatic tools predict that this arginine to glutamine amino acid change would be neutral, and the Arg471 residue at this position is highly conserved across the mammalian species examined. Studies examining the functiol consequence of this variant have not been performed, to our knowledge. At this time, there is insufficient evidence to determine if this variant is pathogenic or benign. Therefore, we consider this a variant of uncertain significance. ACMG Criteria: BP4

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Nov 19, 2024

ClinVar Genomic variation as it relates to human health

NM_001005273.3(CHD3):c.1235G>A (p.Arg412Gln)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...