rs2297518
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000625.4(NOS2):c.1823C>T(p.Ser608Leu) variant causes a missense change. The variant allele was found at a frequency of 0.184 in 1,608,552 control chromosomes in the GnomAD database, including 28,406 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000625.4 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 |
---|---|---|---|---|---|---|---|
NOS2 | NM_000625.4 | c.1823C>T | p.Ser608Leu | missense_variant | 16/27 | ENST00000313735.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOS2 | ENST00000313735.11 | c.1823C>T | p.Ser608Leu | missense_variant | 16/27 | 1 | NM_000625.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.172 AC: 26142AN: 151996Hom.: 2375 Cov.: 33
GnomAD3 exomes AF: 0.177 AC: 44586AN: 251380Hom.: 4216 AF XY: 0.183 AC XY: 24836AN XY: 135860
GnomAD4 exome AF: 0.185 AC: 269171AN: 1456438Hom.: 26033 Cov.: 31 AF XY: 0.186 AC XY: 134655AN XY: 724896
GnomAD4 genome AF: 0.172 AC: 26144AN: 152114Hom.: 2373 Cov.: 33 AF XY: 0.173 AC XY: 12838AN XY: 74374
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 32% of patients studied by a panel of primary immunodeficiencies. Number of patients: 30. Only high quality variants are reported. - |
NOS2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 04, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at