14-105142892-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002226.5(JAG2):c.3520G>A(p.Val1174Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00051 in 1,600,202 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002226.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAG2 | NM_002226.5 | c.3520G>A | p.Val1174Ile | missense_variant | 26/26 | ENST00000331782.8 | NP_002217.3 | |
JAG2 | NM_145159.3 | c.3406G>A | p.Val1136Ile | missense_variant | 25/25 | NP_660142.1 | ||
JAG2 | XM_047431352.1 | c.3178G>A | p.Val1060Ile | missense_variant | 25/25 | XP_047287308.1 | ||
JAG2 | XM_047431353.1 | c.3064G>A | p.Val1022Ile | missense_variant | 24/24 | XP_047287309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG2 | ENST00000331782.8 | c.3520G>A | p.Val1174Ile | missense_variant | 26/26 | 1 | NM_002226.5 | ENSP00000328169 | P1 | |
JAG2 | ENST00000347004.2 | c.3406G>A | p.Val1136Ile | missense_variant | 25/25 | 1 | ENSP00000328566 | |||
JAG2 | ENST00000546616.1 | n.1138G>A | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152206Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000566 AC: 125AN: 221040Hom.: 0 AF XY: 0.000563 AC XY: 68AN XY: 120694
GnomAD4 exome AF: 0.000526 AC: 762AN: 1447880Hom.: 1 Cov.: 30 AF XY: 0.000538 AC XY: 387AN XY: 719196
GnomAD4 genome AF: 0.000355 AC: 54AN: 152322Hom.: 1 Cov.: 34 AF XY: 0.000336 AC XY: 25AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 22, 2023 | BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at