Variant 8-60819983-CTT-CT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_017780.4(CHD7):c.2614-14del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 1,268,764 control chromosomes in the GnomAD database, including 737 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 60 hom., cov: 33)

Exomes 𝑓: 0.023 ( 677 hom. )

Consequence

CHD7
NM_017780.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.127

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 8-60819983-CT-C is Benign according to our data. Variant chr8-60819983-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 210715.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-60819983-CT-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHD7	NM_017780.4 linkuse as main transcript	c.2614-14del		intron_variant		ENST00000423902.7

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
CHD7	ENST00000423902.7 linkuse as main transcript	c.2614-14del	intron_variant	5	NM_017780.4	P1	Q9P2D1-1
CHD7	ENST00000524602.5 linkuse as main transcript	c.1716+38943del	intron_variant	1			Q9P2D1-4
CHD7	ENST00000525508.1 linkuse as main transcript	c.2614-14del	intron_variant	5			Q9P2D1-2
CHD7	ENST00000695853.1 linkuse as main transcript	c.2614-14del	intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0152

AC:

2283

AN:

150312

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00335

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0194

Gnomad ASJ

AF:

0.0293

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.0661

Gnomad FIN

AF:

0.00542

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.0267

GnomAD4 exome

AF:

0.0233

AC:

26014

AN:

1118342

Hom.:

677

Cov.:

AF XY:

0.0252

AC XY:

14028

AN XY:

557744

show subpopulations

Gnomad4 AFR exome

AF:

0.00836

Gnomad4 AMR exome

AF:

0.0259

Gnomad4 ASJ exome

AF:

0.0456

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.0809

Gnomad4 FIN exome

AF:

0.00956

Gnomad4 NFE exome

AF:

0.0139

Gnomad4 OTH exome

AF:

0.0292

GnomAD4 genome

AF:

0.0151

AC:

2275

AN:

150422

Hom.:

Cov.:

AF XY:

0.0166

AC XY:

1218

AN XY:

73402

show subpopulations

Gnomad4 AFR

AF:

0.00332

Gnomad4 AMR

AF:

0.0194

Gnomad4 ASJ

AF:

0.0293

Gnomad4 EAS

AF:

0.119

Gnomad4 SAS

AF:

0.0662

Gnomad4 FIN

AF:

0.00542

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.0279

Alfa

AF:

0.0227

Hom.:

Bravo

AF:

0.0145

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 30, 2023	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Feb 07, 2019	- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 07, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over