rs5906300

chrX-46947342-G-A

Variant summary

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

The NM_014735.5(JADE3):c.-12+34623G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 111,145 control chromosomes in the GnomAD database, including 201 homozygotes. There are 1,728 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 0.051 (201 hom., 1728 hem., cov: 22)
• Consequence: JADE3 NM_014735.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JADE3	NM_014735.5	c.-12+34623G>A		intron_variant		ENST00000614628.5
JADE3	NM_001077445.3	c.-12+35002G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JADE3	ENST00000614628.5	c.-12+34623G>A		intron_variant		1	NM_014735.5	P1
JADE3	ENST00000424392.5	c.-12+35002G>A		intron_variant		3
JADE3	ENST00000455411.1	c.-12+34410G>A		intron_variant		4
JADE3	ENST00000611250.4	c.-12+35002G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 5637 AN: 111096 Hom.: 200 Cov.: 22 AF XY: 0.0517 AC XY: 1723 AN XY: 33338

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.00733

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.00113

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.00837

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0508 AC: 5644 AN: 111145 Hom.: 201 Cov.: 22 AF XY: 0.0517 AC XY: 1728 AN XY: 33397

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0423

Gnomad4 EAS AF: 0.00113

Gnomad4 SAS AF: 0.0364

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.0533

Alfa AF: 0.0615 Hom.: 2930

Bravo AF: 0.0560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.14
Dann	Benign	0.61

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: rs5906300; hg19: chrX-46806777;