14-105168369-CCAG-C
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_002226.5(JAG2):c.49_51delCTG(p.Leu17del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00298 in 985,194 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000069 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0035 ( 0 hom. )
Consequence
JAG2
NM_002226.5 conservative_inframe_deletion
NM_002226.5 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.33
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_002226.5. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAG2 | NM_002226.5 | c.49_51delCTG | p.Leu17del | conservative_inframe_deletion | 1/26 | ENST00000331782.8 | NP_002217.3 | |
JAG2 | NM_145159.3 | c.49_51delCTG | p.Leu17del | conservative_inframe_deletion | 1/25 | NP_660142.1 | ||
JAG2 | XM_047431354.1 | c.49_51delCTG | p.Leu17del | conservative_inframe_deletion | 1/18 | XP_047287310.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG2 | ENST00000331782.8 | c.49_51delCTG | p.Leu17del | conservative_inframe_deletion | 1/26 | 1 | NM_002226.5 | ENSP00000328169.3 | ||
JAG2 | ENST00000347004.2 | c.49_51delCTG | p.Leu17del | conservative_inframe_deletion | 1/25 | 1 | ENSP00000328566.2 | |||
ENSG00000257622 | ENST00000548203.1 | n.67-10609_67-10607delCTG | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000687 AC: 1AN: 145654Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.00350 AC: 2938AN: 839452Hom.: 0 AF XY: 0.00377 AC XY: 1525AN XY: 404600
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GnomAD4 genome AF: 0.00000686 AC: 1AN: 145742Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 70932
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at