16-50697256-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_022162.3(NOD2):āc.13G>Cā(p.Gly5Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000764 in 1,558,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_022162.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOD2 | NM_001370466.1 | c.-8-2232G>C | intron_variant | ENST00000647318.2 | NP_001357395.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000348 AC: 53AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 20AN: 167788Hom.: 0 AF XY: 0.0000451 AC XY: 4AN XY: 88622
GnomAD4 exome AF: 0.0000469 AC: 66AN: 1405840Hom.: 0 Cov.: 31 AF XY: 0.0000375 AC XY: 26AN XY: 694102
GnomAD4 genome AF: 0.000348 AC: 53AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74346
ClinVar
Submissions by phenotype
Regional enteritis;C5201146:Blau syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 07, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at