chr14-105142723-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002226.5(JAG2):āc.3689A>Gā(p.Asn1230Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000066 in 1,607,158 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_002226.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAG2 | NM_002226.5 | c.3689A>G | p.Asn1230Ser | missense_variant | 26/26 | ENST00000331782.8 | NP_002217.3 | |
JAG2 | NM_145159.3 | c.3575A>G | p.Asn1192Ser | missense_variant | 25/25 | NP_660142.1 | ||
JAG2 | XM_047431352.1 | c.3347A>G | p.Asn1116Ser | missense_variant | 25/25 | XP_047287308.1 | ||
JAG2 | XM_047431353.1 | c.3233A>G | p.Asn1078Ser | missense_variant | 24/24 | XP_047287309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAG2 | ENST00000331782.8 | c.3689A>G | p.Asn1230Ser | missense_variant | 26/26 | 1 | NM_002226.5 | ENSP00000328169 | P1 | |
JAG2 | ENST00000347004.2 | c.3575A>G | p.Asn1192Ser | missense_variant | 25/25 | 1 | ENSP00000328566 | |||
JAG2 | ENST00000546616.1 | n.1307A>G | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152030Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000119 AC: 28AN: 235344Hom.: 0 AF XY: 0.000132 AC XY: 17AN XY: 129074
GnomAD4 exome AF: 0.0000674 AC: 98AN: 1455008Hom.: 0 Cov.: 30 AF XY: 0.0000760 AC XY: 55AN XY: 723366
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.3689A>G (p.N1230S) alteration is located in exon 26 (coding exon 26) of the JAG2 gene. This alteration results from a A to G substitution at nucleotide position 3689, causing the asparagine (N) at amino acid position 1230 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at