8-60678764-CGCGGCGGCGGCGGCGGCGGCG-CGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG

Variant names:

• chr8-60678764-C-CGCGGCGGCGGCGGCGGCGGCG
• rs886063023
• NM_017780.4:c.-487_-467dupGGCGGCGGCGGCGGCGGCGGC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_017780.4(CHD7):​c.-487_-467dupGGCGGCGGCGGCGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0017 (2 hom., cov: 0)
• Consequence: CHD7 NM_017780.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

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 Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00174 (239/137574) while in subpopulation AMR AF= 0.00723 (103/14240). AF 95% confidence interval is 0.0061. There are 2 homozygotes in gnomad4. There are 137 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 239 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHD7	NM_017780.4	c.-487_-467dupGGCGGCGGCGGCGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 38	ENST00000423902.7	NP_060250.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD7	ENST00000423902	c.-487_-467dupGGCGGCGGCGGCGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 38	5	NM_017780.4	ENSP00000392028.1

Frequencies

GnomAD3 genomes AF: 0.00174 AC: 240 AN: 137580 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00724

Gnomad ASJ AF: 0.00121

Gnomad EAS AF: 0.00112

Gnomad SAS AF: 0.00224

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000492

Gnomad OTH AF: 0.00106

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00174 AC: 239 AN: 137574 Hom.: 2 Cov.: 0 AF XY: 0.00205 AC XY: 137 AN XY: 66696

Gnomad4 AFR AF: 0.00225

Gnomad4 AMR AF: 0.00723

Gnomad4 ASJ AF: 0.00121

Gnomad4 EAS AF: 0.00113

Gnomad4 SAS AF: 0.00203

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000492

Gnomad4 OTH AF: 0.00106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886063023; hg19: chr8-61591323;