rs7204230

Variant names:

• chr16-53158419-T-C
• rs7204230
• NM_001308319.2:c.1452+878T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CHD9	NM_001308319.2	c.1452+878T>C		intron_variant	Intron 2 of 38	ENST00000447540.6	NP_001295248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD9	ENST00000447540.6	c.1452+878T>C		intron_variant	Intron 2 of 38	5	NM_001308319.2	ENSP00000396345.2

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

African (AFR) AF: 0.332 AC: 13762 AN: 41460

American (AMR) AF: 0.239 AC: 3646 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1264 AN: 3466

East Asian (EAS) AF: 0.252 AC: 1305 AN: 5170

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4818

European-Finnish (FIN) AF: 0.284 AC: 2998 AN: 10554

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21487 AN: 67980

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.316 Hom.: 16115

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
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7204230; hg19: chr16-53192331;