chr17-7903378-AGATGATGCTGAC-A

Variant names:

• chr17-7903378-AGATGATGCTGAC-A
• rs1555612691
• NM_001005273.3:c.3603_3614delGATGATGCTGAC

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM4 PP3 PP5_Moderate

The NM_001005273.3(CHD3):​c.3603_3614delGATGATGCTGAC​(p.Met1202_Thr1205del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHD3 NM_001005273.3 disruptive_inframe_deletion
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 10.0
• Publications: 0 publications found

Genes affected

CHD3 (HGNC:1918): (chromodomain helicase DNA binding protein 3) This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

CHD3 Gene-Disease associations (from GenCC):

• Snijders Blok-Campeau syndrome

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: G2P, Illumina, Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_001005273.3.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 17-7903378-AGATGATGCTGAC-A is Pathogenic according to our data. Variant chr17-7903378-AGATGATGCTGAC-A is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 548030.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005273.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHD3	NM_001005273.3	MANE Select	c.3603_3614delGATGATGCTGAC	p.Met1202_Thr1205del	disruptive_inframe_deletion	Exon 23 of 40	NP_001005273.1
	CHD3	NM_001437504.1		c.3780_3791delGATGATGCTGAC	p.Met1261_Thr1264del	disruptive_inframe_deletion	Exon 23 of 40	NP_001424433.1
	CHD3	NM_001005271.3		c.3780_3791delGATGATGCTGAC	p.Met1261_Thr1264del	disruptive_inframe_deletion	Exon 23 of 40	NP_001005271.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHD3	ENST00000330494.12	TSL:1 MANE Select	c.3603_3614delGATGATGCTGAC	p.Met1202_Thr1205del	disruptive_inframe_deletion	Exon 23 of 40	ENSP00000332628.7
	CHD3	ENST00000358181.8	TSL:1	c.3603_3614delGATGATGCTGAC	p.Met1202_Thr1205del	disruptive_inframe_deletion	Exon 23 of 39	ENSP00000350907.4
	CHD3	ENST00000700753.1		c.3780_3791delGATGATGCTGAC	p.Met1261_Thr1264del	disruptive_inframe_deletion	Exon 23 of 40	ENSP00000515165.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Feb 13, 2018

Mayo Clinic Laboratories, Mayo Clinic

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		10
Mutation Taster		=13/187	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1555612691; hg19: chr17-7806696;