rs5743272
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001370466.1(NOD2):āc.974A>Gā(p.His325Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000704 in 1,614,170 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H325N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001370466.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOD2 | NM_001370466.1 | c.974A>G | p.His325Arg | missense_variant | 4/12 | ENST00000647318.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOD2 | ENST00000647318.2 | c.974A>G | p.His325Arg | missense_variant | 4/12 | NM_001370466.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00356 AC: 542AN: 152162Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000959 AC: 241AN: 251434Hom.: 3 AF XY: 0.000773 AC XY: 105AN XY: 135898
GnomAD4 exome AF: 0.000406 AC: 593AN: 1461890Hom.: 2 Cov.: 39 AF XY: 0.000355 AC XY: 258AN XY: 727246
GnomAD4 genome ? AF: 0.00357 AC: 543AN: 152280Hom.: 2 Cov.: 33 AF XY: 0.00345 AC XY: 257AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 12, 2020 | - - |
Regional enteritis;C5201146:Blau syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Autoinflammatory syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 22, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at