14-105142706-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_002226.5(JAG2):c.3706G>A(p.Gly1236Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00072 in 1,599,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_002226.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAG2 | NM_002226.5 | c.3706G>A | p.Gly1236Ser | missense_variant | 26/26 | ENST00000331782.8 | NP_002217.3 | |
JAG2 | NM_145159.3 | c.3592G>A | p.Gly1198Ser | missense_variant | 25/25 | NP_660142.1 | ||
JAG2 | XM_047431352.1 | c.3364G>A | p.Gly1122Ser | missense_variant | 25/25 | XP_047287308.1 | ||
JAG2 | XM_047431353.1 | c.3250G>A | p.Gly1084Ser | missense_variant | 24/24 | XP_047287309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG2 | ENST00000331782.8 | c.3706G>A | p.Gly1236Ser | missense_variant | 26/26 | 1 | NM_002226.5 | ENSP00000328169 | P1 | |
JAG2 | ENST00000347004.2 | c.3592G>A | p.Gly1198Ser | missense_variant | 25/25 | 1 | ENSP00000328566 | |||
JAG2 | ENST00000546616.1 | n.1324G>A | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000414 AC: 63AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000686 AC: 151AN: 219980Hom.: 0 AF XY: 0.000570 AC XY: 69AN XY: 121052
GnomAD4 exome AF: 0.000752 AC: 1088AN: 1447232Hom.: 0 Cov.: 30 AF XY: 0.000721 AC XY: 518AN XY: 718734
GnomAD4 genome AF: 0.000414 AC: 63AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74484
ClinVar
Submissions by phenotype
JAG2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 04, 2024 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at