rs3852742

Variant names:

• chr16-53098892-G-A
• rs3852742
• NM_001308319.2:c.-165+43815G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001308319.2(CHD9):​c.-165+43815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,228 control chromosomes in the GnomAD database, including 1,296 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 0.11 (1296 hom., cov: 32)
• Consequence: CHD9 NM_001308319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.87
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHD9	NM_001308319.2	c.-165+43815G>A		intron_variant	Intron 1 of 38	ENST00000447540.6	NP_001295248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD9	ENST00000447540.6	c.-165+43815G>A		intron_variant	Intron 1 of 38	5	NM_001308319.2	ENSP00000396345.2
CHD9	ENST00000566029.5	c.-165+43815G>A		intron_variant	Intron 1 of 38	1		ENSP00000457466.1
CHD9	ENST00000615216.4	c.-5061+43815G>A		intron_variant	Intron 1 of 37	5		ENSP00000478361.1
CHD9	ENST00000561869.1	n.40-22408G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16604 AN: 152110 Hom.: 1295 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.109 AC: 16612 AN: 152228 Hom.: 1296 Cov.: 32 AF XY: 0.112 AC XY: 8358 AN XY: 74426

African (AFR) AF: 0.121 AC: 5034 AN: 41544

American (AMR) AF: 0.121 AC: 1858 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3468

East Asian (EAS) AF: 0.428 AC: 2212 AN: 5170

South Asian (SAS) AF: 0.174 AC: 839 AN: 4826

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10600

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0775 AC: 5270 AN: 68008

Other (OTH) AF: 0.0941 AC: 199 AN: 2114

Alfa AF: 0.0911 Hom.: 3604

Bravo AF: 0.114

Asia WGS AF: 0.279 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		2.9
PromoterAI		-0.031	Neutral
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: rs3852742; hg19: chr16-53132804;