chrX-47024648-G-T

Variant names:

• chrX-47024648-G-T
• rs5952987
• NM_014735.5:c.285-76G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014735.5(JADE3):​c.285-76G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: JADE3 NM_014735.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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.285-76G>T		intron	N/A	NP_055550.1
	JADE3	NM_001077445.3		c.285-76G>T		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.285-76G>T		intron	N/A	ENSP00000481850.1
	JADE3	ENST00000611250.4	TSL:2	c.285-76G>T		intron	N/A	ENSP00000479377.1
	JADE3	ENST00000424392.5	TSL:3	c.285-76G>T		intron	N/A	ENSP00000391009.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 481985 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 130475

African (AFR) AF: 0.00 AC: 0 AN: 12900

American (AMR) AF: 0.00 AC: 0 AN: 20188

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11653

East Asian (EAS) AF: 0.00 AC: 0 AN: 24932

South Asian (SAS) AF: 0.00 AC: 0 AN: 28237

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36413

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2696

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 320228

Other (OTH) AF: 0.00 AC: 0 AN: 24738

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.62
PhyloP100		0.52

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: rs5952987; hg19: chrX-46884050;