rs7204230

Positions:

• chr16-53158419-T-C
• chr16-53158419-T-G

Variant summary

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

The NM_001308319.2(CHD9):​c.1452+878T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,036 control chromosomes in the GnomAD database, including 7,494 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 0.31 (7494 hom., cov: 32)
• Consequence: CHD9 NM_001308319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

Genes affected

CHD9 (HGNC:25701): (chromodomain helicase DNA binding protein 9) Predicted to enable ATP binding activity; ATP-dependent activity, acting on DNA; and DNA binding activity. Predicted to be involved in DNA duplex unwinding and chromatin organization. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHD9	NM_001308319.2	c.1452+878T>C		intron_variant		ENST00000447540.6	NP_001295248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHD9	ENST00000447540.6	c.1452+878T>C		intron_variant		5	NM_001308319.2	ENSP00000396345	P4

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47204 AN: 151918 Hom.: 7480 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.311 AC: 47243 AN: 152036 Hom.: 7494 Cov.: 32 AF XY: 0.307 AC XY: 22812 AN XY: 74314

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.326

Alfa AF: 0.323 Hom.: 4840

Bravo AF: 0.306

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.59

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: rs7204230; hg19: chr16-53192331;