12-117247465-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_000620.5(NOS1):c.2706C>T(p.His902His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,611,784 control chromosomes in the GnomAD database, including 82,302 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000620.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS1 | NM_000620.5 | c.2706C>T | p.His902His | synonymous_variant | Exon 18 of 29 | ENST00000317775.11 | NP_000611.1 | |
NOS1 | NM_001204218.2 | c.2808C>T | p.His936His | synonymous_variant | Exon 19 of 30 | NP_001191147.1 | ||
NOS1 | NM_001204213.2 | c.1698C>T | p.His566His | synonymous_variant | Exon 17 of 28 | NP_001191142.1 | ||
NOS1 | NM_001204214.2 | c.1698C>T | p.His566His | synonymous_variant | Exon 17 of 28 | NP_001191143.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOS1 | ENST00000317775.11 | c.2706C>T | p.His902His | synonymous_variant | Exon 18 of 29 | 1 | NM_000620.5 | ENSP00000320758.6 | ||
NOS1 | ENST00000338101.8 | c.2808C>T | p.His936His | synonymous_variant | Exon 18 of 29 | 5 | ENSP00000337459.4 | |||
NOS1 | ENST00000618760.4 | c.2808C>T | p.His936His | synonymous_variant | Exon 19 of 30 | 5 | ENSP00000477999.1 |
Frequencies
GnomAD3 genomes AF: 0.296 AC: 44776AN: 151302Hom.: 7453 Cov.: 30
GnomAD3 exomes AF: 0.350 AC: 86657AN: 247758Hom.: 17160 AF XY: 0.341 AC XY: 45811AN XY: 134432
GnomAD4 exome AF: 0.313 AC: 457509AN: 1460364Hom.: 74825 Cov.: 35 AF XY: 0.313 AC XY: 227195AN XY: 726476
GnomAD4 genome AF: 0.296 AC: 44823AN: 151420Hom.: 7477 Cov.: 30 AF XY: 0.299 AC XY: 22117AN XY: 73932
ClinVar
Submissions by phenotype
NOS1-related disorder Benign:1
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