X-47054092-C-G

Position:

• chrX-47054092-C-G

Variant summary

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

The NM_014735.5(JADE3):​c.973-66C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 756,387 control chromosomes in the GnomAD database, including 8,333 homozygotes. There are 33,924 hemizygotes in GnomAD. 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 0.16 (1276 hom., 5220 hem., cov: 22)
  • Exomes 𝑓: 0.16 (7057 hom. 28704 hem.)
• Consequence: JADE3 NM_014735.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

Genes affected

JADE3 (HGNC:22982): (jade family PHD finger 3) This gene encodes a member of a family of large proteins containing PHD (plant homeo domain)-type zinc fingers. The encoded protein may be associated in a nuclear complex that functions in histone H4 acetylation. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JADE3	NM_014735.5	c.973-66C>G		intron_variant		ENST00000614628.5
JADE3	NM_001077445.3	c.973-66C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JADE3	ENST00000614628.5	c.973-66C>G		intron_variant		1	NM_014735.5	P1
JADE3	ENST00000611250.4	c.973-66C>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 17859 AN: 110401 Hom.: 1273 Cov.: 22 AF XY: 0.160 AC XY: 5222 AN XY: 32671

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.198

GnomAD4 exome AF: 0.156 AC: 100844 AN: 645933 Hom.: 7057 AF XY: 0.167 AC XY: 28704 AN XY: 172345

Gnomad4 AFR exome AF: 0.141

Gnomad4 AMR exome AF: 0.443

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.384

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.165

GnomAD4 genome AF: 0.162 AC: 17862 AN: 110454 Hom.: 1276 Cov.: 22 AF XY: 0.159 AC XY: 5220 AN XY: 32734

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.203

Alfa AF: 0.159 Hom.: 924

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.8
DANN	Benign	0.69

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: rs2239791; hg19: chrX-46913494;