7-150993921-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000603.5(NOS3):c.118C>T(p.Arg40Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000867 in 1,580,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS3 | NM_000603.5 | c.118C>T | p.Arg40Trp | missense_variant | Exon 2 of 27 | ENST00000297494.8 | NP_000594.2 | |
NOS3 | NM_001160111.1 | c.118C>T | p.Arg40Trp | missense_variant | Exon 1 of 14 | NP_001153583.1 | ||
NOS3 | NM_001160110.1 | c.118C>T | p.Arg40Trp | missense_variant | Exon 1 of 14 | NP_001153582.1 | ||
NOS3 | NM_001160109.2 | c.118C>T | p.Arg40Trp | missense_variant | Exon 1 of 14 | NP_001153581.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOS3 | ENST00000297494.8 | c.118C>T | p.Arg40Trp | missense_variant | Exon 2 of 27 | 1 | NM_000603.5 | ENSP00000297494.3 | ||
NOS3 | ENST00000484524.5 | c.118C>T | p.Arg40Trp | missense_variant | Exon 1 of 14 | 1 | ENSP00000420215.1 | |||
NOS3 | ENST00000467517.1 | c.118C>T | p.Arg40Trp | missense_variant | Exon 1 of 14 | 1 | ENSP00000420551.1 | |||
NOS3 | ENST00000461406.5 | c.-148-1282C>T | intron_variant | Intron 1 of 23 | 2 | ENSP00000417143.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000323 AC: 6AN: 185948Hom.: 0 AF XY: 0.00000983 AC XY: 1AN XY: 101718
GnomAD4 exome AF: 0.0000903 AC: 129AN: 1428664Hom.: 0 Cov.: 31 AF XY: 0.0000988 AC XY: 70AN XY: 708210
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152042Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.118C>T (p.R40W) alteration is located in exon 2 (coding exon 1) of the NOS3 gene. This alteration results from a C to T substitution at nucleotide position 118, causing the arginine (R) at amino acid position 40 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