chr14-105142691-G-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_002226.5(JAG2):c.*4C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,590,800 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 0.00028 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00020 ( 0 hom. )
Consequence
JAG2
NM_002226.5 3_prime_UTR
NM_002226.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.74
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 14-105142691-G-A is Benign according to our data. Variant chr14-105142691-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3033613.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAG2 | NM_002226.5 | c.*4C>T | 3_prime_UTR_variant | 26/26 | ENST00000331782.8 | NP_002217.3 | ||
JAG2 | NM_145159.3 | c.*4C>T | 3_prime_UTR_variant | 25/25 | NP_660142.1 | |||
JAG2 | XM_047431352.1 | c.*4C>T | 3_prime_UTR_variant | 25/25 | XP_047287308.1 | |||
JAG2 | XM_047431353.1 | c.*4C>T | 3_prime_UTR_variant | 24/24 | XP_047287309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG2 | ENST00000331782.8 | c.*4C>T | 3_prime_UTR_variant | 26/26 | 1 | NM_002226.5 | ENSP00000328169 | P1 | ||
JAG2 | ENST00000347004.2 | c.*4C>T | 3_prime_UTR_variant | 25/25 | 1 | ENSP00000328566 | ||||
JAG2 | ENST00000546616.1 | n.1339C>T | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152156Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
43
AN:
152156
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000501 AC: 104AN: 207672Hom.: 0 AF XY: 0.000533 AC XY: 61AN XY: 114400
GnomAD3 exomes
AF:
AC:
104
AN:
207672
Hom.:
AF XY:
AC XY:
61
AN XY:
114400
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000196 AC: 282AN: 1438526Hom.: 0 Cov.: 29 AF XY: 0.000231 AC XY: 165AN XY: 713744
GnomAD4 exome
AF:
AC:
282
AN:
1438526
Hom.:
Cov.:
29
AF XY:
AC XY:
165
AN XY:
713744
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000282 AC: 43AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74448
GnomAD4 genome
AF:
AC:
43
AN:
152274
Hom.:
Cov.:
33
AF XY:
AC XY:
30
AN XY:
74448
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
16
AN:
3478
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 | Sep 10, 2019 | 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
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at