rs794727423

Positions:

• chr8-60850476-G-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PP3_Moderate PP5_Very_Strong

The NM_017780.4(CHD7):​c.5405-17G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CHD7 NM_017780.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:14
• Conservation: PhyloP100: 0.687

Genes affected

CHD7 (HGNC:20626): (chromodomain helicase DNA binding protein 7) This gene encodes a protein that contains several helicase family domains. Mutations in this gene have been found in some patients with the CHARGE syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 8-60850476-G-A is Pathogenic according to our data. Variant chr8-60850476-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 195978.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60850476-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHD7	NM_017780.4	c.5405-17G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000423902.7	NP_060250.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHD7	ENST00000423902.7	c.5405-17G>A		splice_polypyrimidine_tract_variant, intron_variant		5	NM_017780.4	ENSP00000392028	P1
CHD7	ENST00000524602.5	c.1717-11753G>A		intron_variant		1		ENSP00000437061
CHD7	ENST00000695853.1	c.5405-17G>A		splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant				ENSP00000512218

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1441278 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 712320

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:14

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 27, 2018	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2022	CHD7: PS2, PM2, PS3:Moderate, PS4:Moderate -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Nov 05, 2020	This variant appears to occur de novo in a patient tested at Athena Diagnostics and in previously reported individuals with CHARGE syndrome (PMID: 32326958, 22033296, 30176936, 16155193). This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Computational tools yielded predictions that this variant may result in the gain of a cryptic splice site resulting in the insertion of five amino acid residues (PMID 29255276).This observation is not an independent occurrence and has been identified in the same individual by RCIGM, the other laboratory participating in the GEMINI study. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 19, 2023	Published functional studies show variant leads to an in-frame insertion of 5 amino acids in a non-repeat region (Vuorela et al., 2007; Legendre et al., 2018); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31965297, 18073582, 26411921, 22033296, 16155193, 26538304, 27321065, 14626219, 28492532, 29255276, 15666308, 31289371, 22539353, 23849776, 26544072, 26590800, 25472840, 17661815, 22461308, 21532573, 21378379, 20186815, 20130577, 17299439, 10590394, 16400610, 18834967, 29304373, 15300250, 31216405, 30176936, 32411386, 32326958, 35904121, 33502061, 36151134) -

CHARGE syndrome Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	May 06, 2021	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with CHARGE syndrome (MIM#214800) and hypogonadotropic hypogonadism 5 with or without anosmia (MIM#612370). The genotype-phenotype correlation is currently unestablished. (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0209 - Splice site variant proven to affect splicing of the transcript with uncertain effect on protein sequence. Although the variant does not lie within the splice site region of intron 25, a minigene assay demonstrated activation of a cryptic splice site. An inframe insertion of 5 amino acids was predicted (p.(His1801_Gly1802insAspGlyHisGlyThr)) (PMID: 29255276). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0508 - In silico predictions for abnormal splicing are conflicting. However, it is important to note that these tools are not optimized for variants beyond the splice region. (I) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants. Intron 25 has been described as a hotspot for intronic variants due to the presence of a distant splicing branch point (PMID: 29255276). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in at least ten individuals with CHARGE syndrome, several of whom were proven to be de novo for this variant (PMID: 29255276; ClinVar). (SP) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis)]. (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Mar 22, 2022	The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000195978) It has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 18073582, 16155193, 22033296, 26544072, 3bilion dataset). In silico tools predict the variant to alter splicing and produce an abnormal transcript (SPLICEAI: 1.0>=0.8). It is not observed in the gnomAD v2.1.1 dataset. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 08, 2023	This sequence change falls in intron 25 of the CHD7 gene. It does not directly change the encoded amino acid sequence of the CHD7 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with CHARGE syndrome (PMID: 16155193, 22033296, 26538304, 26544072). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 195978). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	in vitro	Laboratoire de Genetique Biologique, CHU de Poitiers	May 05, 2017	Found de novo on many CHARGE syndrome Patients. Minigene assays confirm the pathogenic effect on splicing mechanism -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Molecular Medicine, Children’s Hospital of Fudan University	May 10, 2019	- -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 21, 2017

The c.5405-17G>A intronic variant results from a G to A substitution 17 nucleotides upstream from coding exon 25 in the CHD7 gene. This variant was identified in multiple individuals with a clinical diagnosis of CHARGE syndrome, including three de novo occurrences; however, paternity was not confirmed (Jongmans MC et al. J. Med. Genet., 2006 Apr;43:306-14; Vuorela P et al. Genet. Med., 2007 Oct;9:690-4; Bergman JE et al. J. Pediatr., 2011 Mar;158:474-9; Bilan F et al. J Mol Diagn, 2012 Jan;14:46-55; Wong MT et al. PLoS ONE, 2015 Nov;10:e0142350; Sohn YB et al. J. Hum. Genet., 2016 Mar;61:235-9). This nucleotide position is poorly conserved in available vertebrate species. Using the Human Splicing Finder (HSF) and Maximum Entropy Principle (MaxEnt) splice site prediction tools, this alteration is predicted to create a new alternate splice donor site (Desmet FO et al. Nucleic Acids Res. 2009 May;37:e67; Yeo G et al J Comput Biol. 2004;11(2-3):377-94). Analysis of mRNA from the cells of an affected individual showed that this alteration creates a cryptic splice site resulting in the addition of 15 nucleotides (Vuorela P et al. Genet. Med., 2007 Oct;9:690-4). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

CHARGE syndrome;C3552553:Hypogonadotropic hypogonadism 5 with or without anosmia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Dec 31, 2017

- -

Hypogonadotropic hypogonadism 5 with or without anosmia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 24, 2023

Variant summary: CHD7 c.5405-17G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Four predict the variant creates a 3 acceptor site. Multiple reports have shown experimental evidence that this variant affects mRNA splicing and activates the alternative 3 splice site (examples: Aref-Eshgh_2018 and Legendre_2018). The variant was absent in 246432 control chromosomes (gnomAD). c.5405-17G>A has been reported in the literature in multiple individuals affected with CHARGE syndrome (examples: Jongmans_2006, Janssen_2012, Aref-Eshgh_AJHG_2018, Wang_2020). Additionally, each of these publications have reported at-least one case as a de novo occurrence (examples: Jongmans_2006, Janssen_2012, Aref-Eshgh_AJHG_2018, Wang_2020). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 29255276, 29304373, 22461308, 16155193, 31965297). Eleven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		1.0		Position offset: 2
DS_AL_spliceai		0.96		Position offset: 17

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

Publications

LitVar

Other links and lift over

dbSNP: rs794727423; hg19: chr8-61763035;