NM_017780.4:c.191_194delCAAA

Variant names:

• chr8-60741618-TCAAA-T
• rs587783431
• NM_017780.4:c.191_194delCAAA

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_017780.4(CHD7):​c.191_194delCAAA​(p.Thr64SerfsTer2) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHD7 NM_017780.4 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 7.77
• Publications: 2 publications found

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]

CHD7 Gene-Disease associations (from GenCC):

• CHARGE syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, PanelApp Australia, Broad Center for Mendelian Genomics, ClinGen, G2P
• hypogonadotropic hypogonadism 5 with or without anosmia

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• hypogonadotropic hypogonadism

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Kallmann syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Omenn syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 8-60741618-TCAAA-T is Pathogenic according to our data. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60741618-TCAAA-T is described in CliVar as Pathogenic. Clinvar id is 158281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHD7	NM_017780.4	c.191_194delCAAA	p.Thr64SerfsTer2	frameshift_variant	Exon 2 of 38	ENST00000423902.7	NP_060250.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD7	ENST00000423902.7	c.191_194delCAAA	p.Thr64SerfsTer2	frameshift_variant	Exon 2 of 38	5	NM_017780.4	ENSP00000392028.1

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: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

CHARGE syndrome Pathogenic:2

Jul 04, 2023

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with CHD7 related disorder (ClinVar ID: VCV000158281 /PMID: 21158681). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.8
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs587783431; hg19: chr8-61654177;