NM_014697.3:c.346A>G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014697.3(NOS1AP):āc.346A>Gā(p.Ile116Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,640 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014697.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS1AP | NM_014697.3 | c.346A>G | p.Ile116Val | missense_variant, splice_region_variant | Exon 5 of 10 | ENST00000361897.10 | NP_055512.1 | |
NOS1AP | NM_001164757.2 | c.331A>G | p.Ile111Val | missense_variant, splice_region_variant | Exon 5 of 10 | NP_001158229.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOS1AP | ENST00000361897.10 | c.346A>G | p.Ile116Val | missense_variant, splice_region_variant | Exon 5 of 10 | 1 | NM_014697.3 | ENSP00000355133.5 | ||
NOS1AP | ENST00000530878.5 | c.331A>G | p.Ile111Val | missense_variant, splice_region_variant | Exon 5 of 10 | 1 | ENSP00000431586.1 | |||
NOS1AP | ENST00000430120.3 | n.331A>G | splice_region_variant, non_coding_transcript_exon_variant | Exon 5 of 11 | 1 | ENSP00000396713.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251274Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135796
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457640Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 725424
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.346A>G (p.I116V) alteration is located in exon 5 (coding exon 5) of the NOS1AP gene. This alteration results from a A to G substitution at nucleotide position 346, causing the isoleucine (I) at amino acid position 116 to be replaced by a valine (V). 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