Genetic Variant JADE3:c.973-66C>A (chrX-47054092-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014735.5(JADE3):c.973-66C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000155 in 646,658 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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: not found (cov: 22)

Exomes 𝑓: 0.0000015 ( 0 hom. 0 hem. )

Consequence

JADE3
NM_014735.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.223

Publications

5 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: 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=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JADE3	NM_014735.5 link	c.973-66C>A		intron_variant	Intron 8 of 10	ENST00000614628.5	NP_055550.1	Q92613A0A024R1A2
JADE3	NM_001077445.3 link	c.973-66C>A		intron_variant	Intron 8 of 10		NP_001070913.1	Q92613A0A024R1A2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JADE3	ENST00000614628.5 link	c.973-66C>A		intron_variant	Intron 8 of 10	1	NM_014735.5	ENSP00000481850.1		Q92613
JADE3	ENST00000611250.4 link	c.973-66C>A		intron_variant	Intron 8 of 10	2		ENSP00000479377.1		Q92613

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000155

AC:

AN:

646658

Hom.:

AF XY:

0.00

AC XY:

AN XY:

172424

show subpopulations

African (AFR)

AF:

0.0000622

AC:

AN:

16077

American (AMR)

AF:

0.00

AC:

AN:

19565

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12621

East Asian (EAS)

AF:

0.00

AC:

AN:

26581

South Asian (SAS)

AF:

0.00

AC:

AN:

34126

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35509

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1992

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

469940

Other (OTH)

AF:

0.00

AC:

AN:

30247

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.7

(source)

DANN

Benign

0.74

PhyloP100

-0.22

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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over