8-60791496-C-T

Position:

• chr8-60791496-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017780.4(CHD7):​c.2097-3490C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,218 control chromosomes in the GnomAD database, including 25,539 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (25539 hom., cov: 33)
• Consequence: CHD7 NM_017780.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHD7	NM_017780.4	c.2097-3490C>T		intron_variant		ENST00000423902.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHD7	ENST00000423902.7	c.2097-3490C>T		intron_variant		5	NM_017780.4	P1

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80205 AN: 152100 Hom.: 25532 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.539

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.527 AC: 80220 AN: 152218 Hom.: 25539 Cov.: 33 AF XY: 0.536 AC XY: 39907 AN XY: 74434

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.538

Alfa AF: 0.587 Hom.: 3652

Bravo AF: 0.504

Asia WGS AF: 0.682 AC: 2367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs13280978; hg19: chr8-61704055;