Variant 8-60678764-CGCGGCGGCGGCGGCGGCGGCG-CGCGGCGGCGGCGGCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_017780.4(CHD7):c.-472_-467delGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00931 in 138,184 control chromosomes in the GnomAD database, including 12 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0091 ( 10 hom., cov: 0)

Exomes 𝑓: 0.047 ( 2 hom. )

Consequence

CHD7
NM_017780.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.88

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 -8 ACMG points.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00914 (1257/137570) while in subpopulation SAS AF= 0.0352 (156/4434). AF 95% confidence interval is 0.0307. There are 10 homozygotes in gnomad4. There are 615 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1257 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHD7	NM_017780.4 link	c.-472_-467delGGCGGC		5_prime_UTR_variant	Exon 1 of 38	ENST00000423902.7	NP_060250.2	Q9P2D1-1Q6ZWF9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD7	ENST00000423902 link	c.-472_-467delGGCGGC		5_prime_UTR_variant	Exon 1 of 38	5	NM_017780.4	ENSP00000392028.1		Q9P2D1-1

Frequencies

GnomAD3 genomes

AF:

0.00911

AC:

1254

AN:

137576

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00252

Gnomad AMI

AF:

0.0141

Gnomad AMR

AF:

0.0178

Gnomad ASJ

AF:

0.00544

Gnomad EAS

AF:

0.000674

Gnomad SAS

AF:

0.0348

Gnomad FIN

AF:

0.00353

Gnomad MID

AF:

0.0176

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.00798

GnomAD4 exome

AF:

0.0472

AC:

AN:

614

Hom.:

AF XY:

0.0313

AC XY:

AN XY:

352

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0522

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0361

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.00914

AC:

1257

AN:

137570

Hom.:

Cov.:

AF XY:

0.00922

AC XY:

615

AN XY:

66694

show subpopulations

Gnomad4 AFR

AF:

0.00252

Gnomad4 AMR

AF:

0.0179

Gnomad4 ASJ

AF:

0.00544

Gnomad4 EAS

AF:

0.000677

Gnomad4 SAS

AF:

0.0352

Gnomad4 FIN

AF:

0.00353

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.00793

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over