16-50711152-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001370466.1(NOD2):c.1160A>G(p.Asn387Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000836 in 1,614,004 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 (★★).
Frequency
Consequence
NM_001370466.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOD2 | NM_001370466.1 | c.1160A>G | p.Asn387Ser | missense_variant | Exon 4 of 12 | ENST00000647318.2 | NP_001357395.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251288Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135856
GnomAD4 exome AF: 0.0000855 AC: 125AN: 1461832Hom.: 0 Cov.: 39 AF XY: 0.0000798 AC XY: 58AN XY: 727216
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not provided Uncertain:1
BS1 -
Regional enteritis;C5201146:Blau syndrome Uncertain:1
This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 414 of the NOD2 protein (p.Asn414Ser). This variant is present in population databases (rs104895429, gnomAD 0.02%). This missense change has been observed in individual(s) with Crohn disease or spondylarthropathy (PMID: 11875755, 12115249). ClinVar contains an entry for this variant (Variation ID: 97824). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt NOD2 protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects NOD2 function (PMID: 12626759). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Yao syndrome;C5201146:Blau syndrome;CN260071:Inflammatory bowel disease 1 Uncertain:1
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Blau syndrome Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at