7-150996452-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000603.5(NOS3):c.319C>T(p.Arg107Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,428,016 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_000603.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS3 | NM_000603.5 | c.319C>T | p.Arg107Trp | missense_variant | 4/27 | ENST00000297494.8 | NP_000594.2 | |
NOS3 | NM_001160111.1 | c.319C>T | p.Arg107Trp | missense_variant | 3/14 | NP_001153583.1 | ||
NOS3 | NM_001160110.1 | c.319C>T | p.Arg107Trp | missense_variant | 3/14 | NP_001153582.1 | ||
NOS3 | NM_001160109.2 | c.319C>T | p.Arg107Trp | missense_variant | 3/14 | NP_001153581.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOS3 | ENST00000297494.8 | c.319C>T | p.Arg107Trp | missense_variant | 4/27 | 1 | NM_000603.5 | ENSP00000297494.3 | ||
NOS3 | ENST00000484524.5 | c.319C>T | p.Arg107Trp | missense_variant | 3/14 | 1 | ENSP00000420215.1 | |||
NOS3 | ENST00000467517.1 | c.319C>T | p.Arg107Trp | missense_variant | 3/14 | 1 | ENSP00000420551.1 | |||
NOS3 | ENST00000461406.5 | c.-37+1138C>T | intron_variant | 2 | ENSP00000417143.1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.0000879 AC: 17AN: 193356Hom.: 0 AF XY: 0.0000858 AC XY: 9AN XY: 104882
GnomAD4 exome AF: 0.0000217 AC: 31AN: 1428016Hom.: 0 Cov.: 34 AF XY: 0.0000226 AC XY: 16AN XY: 707264
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 01, 2024 | The c.319C>T (p.R107W) alteration is located in exon 4 (coding exon 3) of the NOS3 gene. This alteration results from a C to T substitution at nucleotide position 319, causing the arginine (R) at amino acid position 107 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at