Variant 14-105168369-CCAG-CCAGCAGCAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_002226.5(JAG2):c.46_51dupCTGCTG(p.Leu16_Leu17dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

JAG2
NM_002226.5 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.245

Variant links:

Genes affected

JAG2 (HGNC:6189): (jagged canonical Notch ligand 2) The Notch signaling pathway is an intercellular signaling mechanism that is essential for proper embryonic development. Members of the Notch gene family encode transmembrane receptors that are critical for various cell fate decisions. The protein encoded by this gene is one of several ligands that activate Notch and related receptors. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

JAG2 links:

ENSG00000257622 (HGNC:):

ENSG00000257622 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_002226.5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAG2	NM_002226.5 linkuse as main transcript	c.46_51dupCTGCTG	p.Leu16_Leu17dup	conservative_inframe_insertion	1/26	ENST00000331782.8	NP_002217.3	Q9Y219-1
JAG2	NM_145159.3 linkuse as main transcript	c.46_51dupCTGCTG	p.Leu16_Leu17dup	conservative_inframe_insertion	1/25		NP_660142.1	Q9Y219-2
JAG2	XM_047431354.1 linkuse as main transcript	c.46_51dupCTGCTG	p.Leu16_Leu17dup	conservative_inframe_insertion	1/18		XP_047287310.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
JAG2	ENST00000331782.8 linkuse as main transcript	c.46_51dupCTGCTG	p.Leu16_Leu17dup	conservative_inframe_insertion	1/26	1	NM_002226.5	ENSP00000328169.3	Q9Y219-1
JAG2	ENST00000347004.2 linkuse as main transcript	c.46_51dupCTGCTG	p.Leu16_Leu17dup	conservative_inframe_insertion	1/25	1		ENSP00000328566.2	Q9Y219-2
ENSG00000257622	ENST00000548203.1 linkuse as main transcript	n.67-10612_67-10607dupCTGCTG		intron_variant		3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

866616

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

418392

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over