chrX-46947342-G-A

Variant names:

• chrX-46947342-G-A
• rs5906300
• NM_014735.5:c.-12+34623G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014735.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JADE3	NM_014735.5	MANE Select	c.-12+34623G>A		intron	N/A	NP_055550.1
	JADE3	NM_001077445.3		c.-12+35002G>A		intron	N/A	NP_001070913.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JADE3	ENST00000614628.5	TSL:1 MANE Select	c.-12+34623G>A		intron	N/A	ENSP00000481850.1
	JADE3	ENST00000611250.4	TSL:2	c.-12+35002G>A		intron	N/A	ENSP00000479377.1
	JADE3	ENST00000424392.5	TSL:3	c.-12+35002G>A		intron	N/A	ENSP00000391009.1

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 5637 AN: 111096 Hom.: 200 Cov.: 22

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

African (AFR) AF: 0.0109 AC: 333 AN: 30648

American (AMR) AF: 0.150 AC: 1557 AN: 10392

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 112 AN: 2645

East Asian (EAS) AF: 0.00113 AC: 4 AN: 3525

South Asian (SAS) AF: 0.0364 AC: 95 AN: 2608

European-Finnish (FIN) AF: 0.0585 AC: 349 AN: 5970

Middle Eastern (MID) AF: 0.00917 AC: 2 AN: 218

European-Non Finnish (NFE) AF: 0.0587 AC: 3106 AN: 52938

Other (OTH) AF: 0.0533 AC: 81 AN: 1519

Alfa AF: 0.0600 Hom.: 4031

Bravo AF: 0.0560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.61
PhyloP100		-1.5
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: rs5906300; hg19: chrX-46806777;