14-105142777-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_002226.5(JAG2):c.3635C>T(p.Pro1212Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000178 in 1,610,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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
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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.3635C>T | p.Pro1212Leu | missense_variant | 26/26 | ENST00000331782.8 | NP_002217.3 | |
JAG2 | NM_145159.3 | c.3521C>T | p.Pro1174Leu | missense_variant | 25/25 | NP_660142.1 | ||
JAG2 | XM_047431352.1 | c.3293C>T | p.Pro1098Leu | missense_variant | 25/25 | XP_047287308.1 | ||
JAG2 | XM_047431353.1 | c.3179C>T | p.Pro1060Leu | missense_variant | 24/24 | XP_047287309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG2 | ENST00000331782.8 | c.3635C>T | p.Pro1212Leu | missense_variant | 26/26 | 1 | NM_002226.5 | ENSP00000328169 | P1 | |
JAG2 | ENST00000347004.2 | c.3521C>T | p.Pro1174Leu | missense_variant | 25/25 | 1 | ENSP00000328566 | |||
JAG2 | ENST00000546616.1 | n.1253C>T | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000874 AC: 133AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000246 AC: 60AN: 243982Hom.: 0 AF XY: 0.000210 AC XY: 28AN XY: 133094
GnomAD4 exome AF: 0.000104 AC: 151AN: 1458518Hom.: 0 Cov.: 30 AF XY: 0.000103 AC XY: 75AN XY: 725416
GnomAD4 genome AF: 0.000893 AC: 136AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000886 AC XY: 66AN XY: 74492
ClinVar
Submissions by phenotype
JAG2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 17, 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at