17-27760628-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000625.4(NOS2):c.3005A>T(p.His1002Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000425 in 1,553,656 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000625.4 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 | UniProt |
---|---|---|---|---|---|---|---|
NOS2 | NM_000625.4 | c.3005A>T | p.His1002Leu | missense_variant | 24/27 | ENST00000313735.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOS2 | ENST00000313735.11 | c.3005A>T | p.His1002Leu | missense_variant | 24/27 | 1 | NM_000625.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000119 AC: 19AN: 159740Hom.: 2 AF XY: 0.000190 AC XY: 16AN XY: 84430
GnomAD4 exome AF: 0.0000450 AC: 63AN: 1401340Hom.: 2 Cov.: 32 AF XY: 0.0000752 AC XY: 52AN XY: 691476
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.3005A>T (p.H1002L) alteration is located in exon 24 (coding exon 23) of the NOS2 gene. This alteration results from a A to T substitution at nucleotide position 3005, causing the histidine (H) at amino acid position 1002 to be replaced by a leucine (L). 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