14-105142944-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_002226.5(JAG2):c.3468G>A(p.Pro1156=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000367 in 1,608,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000034 ( 0 hom. )
Consequence
JAG2
NM_002226.5 synonymous
NM_002226.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.574
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 14-105142944-C-T is Benign according to our data. Variant chr14-105142944-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3057429.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.574 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAG2 | NM_002226.5 | c.3468G>A | p.Pro1156= | synonymous_variant | 26/26 | ENST00000331782.8 | NP_002217.3 | |
JAG2 | NM_145159.3 | c.3354G>A | p.Pro1118= | synonymous_variant | 25/25 | NP_660142.1 | ||
JAG2 | XM_047431352.1 | c.3126G>A | p.Pro1042= | synonymous_variant | 25/25 | XP_047287308.1 | ||
JAG2 | XM_047431353.1 | c.3012G>A | p.Pro1004= | synonymous_variant | 24/24 | XP_047287309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG2 | ENST00000331782.8 | c.3468G>A | p.Pro1156= | synonymous_variant | 26/26 | 1 | NM_002226.5 | ENSP00000328169 | P1 | |
JAG2 | ENST00000347004.2 | c.3354G>A | p.Pro1118= | synonymous_variant | 25/25 | 1 | ENSP00000328566 | |||
JAG2 | ENST00000546616.1 | n.1086G>A | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152190Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000171 AC: 40AN: 233564Hom.: 0 AF XY: 0.000116 AC XY: 15AN XY: 129006
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GnomAD4 exome AF: 0.0000336 AC: 49AN: 1456618Hom.: 0 Cov.: 30 AF XY: 0.0000276 AC XY: 20AN XY: 724292
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152190Hom.: 0 Cov.: 34 AF XY: 0.0000941 AC XY: 7AN XY: 74354
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
JAG2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 02, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at