Variant 8-60678764-C-CGCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_017780.4(CHD7):c.-469_-467dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.65 ( 29156 hom., cov: 0)

Exomes 𝑓: 0.49 ( 54 hom. )

Consequence

CHD7
NM_017780.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:2

Conservation

PhyloP100: 0.400

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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.-469_-467dup		5_prime_UTR_variant	1/38	ENST00000423902.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHD7	ENST00000423902.7 linkuse as main transcript	c.-469_-467dup	5_prime_UTR_variant	1/38	5	NM_017780.4	P1	Q9P2D1-1
CHD7	ENST00000695848.1 linkuse as main transcript	n.45_47dup	non_coding_transcript_exon_variant	1/7
CHD7	ENST00000695849.1 linkuse as main transcript	n.45_47dup	non_coding_transcript_exon_variant	1/7
CHD7	ENST00000695853.1 linkuse as main transcript	c.-469_-467dup	5_prime_UTR_variant, NMD_transcript_variant	1/37

Frequencies

GnomAD3 genomes

AF:

0.650

AC:

89392

AN:

137434

Hom.:

29162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.624

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.644

Gnomad EAS

AF:

0.693

Gnomad SAS

AF:

0.692

Gnomad FIN

AF:

0.733

Gnomad MID

AF:

0.521

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.648

GnomAD4 exome

AF:

0.493

AC:

299

AN:

606

Hom.:

Cov.:

AF XY:

0.503

AC XY:

174

AN XY:

346

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.750

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.563

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.351

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.650

AC:

89378

AN:

137426

Hom.:

29156

Cov.:

AF XY:

0.658

AC XY:

43859

AN XY:

66620

show subpopulations

Gnomad4 AFR

AF:

0.655

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.644

Gnomad4 EAS

AF:

0.693

Gnomad4 SAS

AF:

0.692

Gnomad4 FIN

AF:

0.733

Gnomad4 NFE

AF:

0.629

Gnomad4 OTH

AF:

0.649

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

CHARGE syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Hypogonadism with anosmia

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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