chr14-105142937-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002226.5(JAG2):​c.3475C>T​(p.Arg1159Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000472 in 1,608,566 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1159H) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000047 ( 0 hom. )

Consequence

JAG2
NM_002226.5 missense

Scores

1
6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.833
Variant links:
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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12464866).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
JAG2NM_002226.5 linkuse as main transcriptc.3475C>T p.Arg1159Cys missense_variant 26/26 ENST00000331782.8 NP_002217.3
JAG2NM_145159.3 linkuse as main transcriptc.3361C>T p.Arg1121Cys missense_variant 25/25 NP_660142.1
JAG2XM_047431352.1 linkuse as main transcriptc.3133C>T p.Arg1045Cys missense_variant 25/25 XP_047287308.1
JAG2XM_047431353.1 linkuse as main transcriptc.3019C>T p.Arg1007Cys missense_variant 24/24 XP_047287309.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
JAG2ENST00000331782.8 linkuse as main transcriptc.3475C>T p.Arg1159Cys missense_variant 26/261 NM_002226.5 ENSP00000328169 P1Q9Y219-1
JAG2ENST00000347004.2 linkuse as main transcriptc.3361C>T p.Arg1121Cys missense_variant 25/251 ENSP00000328566 Q9Y219-2
JAG2ENST00000546616.1 linkuse as main transcriptn.1093C>T non_coding_transcript_exon_variant 7/75

Frequencies

GnomAD3 genomes
AF:
0.0000460
AC:
7
AN:
152192
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000516
AC:
12
AN:
232386
Hom.:
0
AF XY:
0.0000623
AC XY:
8
AN XY:
128470
show subpopulations
Gnomad AFR exome
AF:
0.000146
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000172
Gnomad SAS exome
AF:
0.000133
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000297
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000474
AC:
69
AN:
1456256
Hom.:
0
Cov.:
30
AF XY:
0.0000483
AC XY:
35
AN XY:
724072
show subpopulations
Gnomad4 AFR exome
AF:
0.0000900
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000986
Gnomad4 SAS exome
AF:
0.000105
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000153
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000460
AC:
7
AN:
152310
Hom.:
0
Cov.:
33
AF XY:
0.0000403
AC XY:
3
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.0000653
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000378
ESP6500AA
AF:
0.000230
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000677
AC:
8
Asia WGS
AF:
0.000289
AC:
1
AN:
3476
EpiCase
AF:
0.000109
EpiControl
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 31, 2023The c.3475C>T (p.R1159C) alteration is located in exon 26 (coding exon 26) of the JAG2 gene. This alteration results from a C to T substitution at nucleotide position 3475, causing the arginine (R) at amino acid position 1159 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.26
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.47
T;.
Eigen
Benign
-0.56
Eigen_PC
Benign
-0.50
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.79
T;T
M_CAP
Pathogenic
0.36
D
MetaRNN
Benign
0.12
T;T
MetaSVM
Benign
-0.45
T
MutationAssessor
Benign
1.8
L;.
MutationTaster
Benign
1.0
N;N
PrimateAI
Uncertain
0.69
T
PROVEAN
Uncertain
-2.8
D;D
REVEL
Benign
0.24
Sift
Uncertain
0.023
D;D
Sift4G
Uncertain
0.018
D;D
Polyphen
0.0060
B;B
Vest4
0.089
MVP
0.61
MPC
0.32
ClinPred
0.054
T
GERP RS
3.6
Varity_R
0.14
gMVP
0.073

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs188092112; hg19: chr14-105609274; API