dbSNP rs5952987: JADE3:c.285-76G>A (chrX-47024648-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014735.5(JADE3):c.285-76G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 593,045 control chromosomes in the GnomAD database, including 8,399 homozygotes. There are 29,507 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 0.21 ( 2036 hom., 6835 hem., cov: 23)

Exomes 𝑓: 0.17 ( 6363 hom. 22672 hem. )

Consequence

JADE3
NM_014735.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.522

Publications

4 publications found

Variant links:

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]

JADE3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JADE3	NM_014735.5	MANE Select	c.285-76G>A		intron	N/A	NP_055550.1	Q92613
	JADE3	NM_001077445.3		c.285-76G>A		intron	N/A	NP_001070913.1	Q92613

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
JADE3	ENST00000614628.5	TSL:1 MANE Select	c.285-76G>A	intron	N/A	ENSP00000481850.1	Q92613
JADE3	ENST00000611250.4	TSL:2	c.285-76G>A	intron	N/A	ENSP00000479377.1	Q92613
JADE3	ENST00000424392.5	TSL:3	c.285-76G>A	intron	N/A	ENSP00000391009.1	F2Z3N8

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

22911

AN:

111612

Hom.:

2034

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.131

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.367

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.223

GnomAD4 exome

AF:

0.166

AC:

79765

AN:

481378

Hom.:

6363

AF XY:

0.174

AC XY:

22672

AN XY:

130402

show subpopulations

African (AFR)

AF:

0.290

AC:

3733

AN:

12881

American (AMR)

AF:

0.451

AC:

9077

AN:

20111

Ashkenazi Jewish (ASJ)

AF:

0.142

AC:

1659

AN:

11645

East Asian (EAS)

AF:

0.383

AC:

9540

AN:

24901

South Asian (SAS)

AF:

0.219

AC:

6185

AN:

28208

European-Finnish (FIN)

AF:

0.143

AC:

5189

AN:

36395

Middle Eastern (MID)

AF:

0.162

AC:

436

AN:

2692

European-Non Finnish (NFE)

AF:

0.124

AC:

39556

AN:

319831

Other (OTH)

AF:

0.178

AC:

4390

AN:

24714

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2352

4704

7056

9408

11760

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1034

2068

3102

4136

5170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.205

AC:

22933

AN:

111667

Hom.:

2036

Cov.:

AF XY:

0.202

AC XY:

6835

AN XY:

33875

show subpopulations

African (AFR)

AF:

0.295

AC:

9046

AN:

30716

American (AMR)

AF:

0.333

AC:

3508

AN:

10541

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

361

AN:

2644

East Asian (EAS)

AF:

0.366

AC:

1289

AN:

3519

South Asian (SAS)

AF:

0.214

AC:

578

AN:

2698

European-Finnish (FIN)

AF:

0.143

AC:

864

AN:

6047

Middle Eastern (MID)

AF:

0.153

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.128

AC:

6821

AN:

53094

Other (OTH)

AF:

0.228

AC:

344

AN:

1512

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

625

1251

1876

2502

3127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.172

Hom.:

15316

Bravo

AF:

0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.0

(source)

DANN

Benign

0.42

PhyloP100

0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over