rs10852453

Positions:

• chr16-53039876-T-A
• chr16-53039876-T-G

Variant summary

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

The ENST00000562178.1(CHD9NB):​n.193-3915A>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 151,826 control chromosomes in the GnomAD database, including 21,405 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 (21405 hom., cov: 31)
• Consequence: CHD9NB ENST00000562178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559

Genes affected

CHD9NB (HGNC:53436): (CHD9 neighbor)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHD9NB	NR_136518.1	n.193-3915A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHD9NB	ENST00000562178.1	n.193-3915A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80027 AN: 151708 Hom.: 21388 Cov.: 31

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.527 AC: 80085 AN: 151826 Hom.: 21405 Cov.: 31 AF XY: 0.527 AC XY: 39108 AN XY: 74162

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.543

Alfa AF: 0.337 Hom.: 748

Bravo AF: 0.538

Asia WGS AF: 0.590 AC: 2047 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10852453; hg19: chr16-53073788;