chr3-16303467-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138381.5(OXNAD1):c.844A>C(p.Ile282Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,613,938 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_138381.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OXNAD1 | NM_138381.5 | c.844A>C | p.Ile282Leu | missense_variant | 9/9 | ENST00000285083.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OXNAD1 | ENST00000285083.10 | c.844A>C | p.Ile282Leu | missense_variant | 9/9 | 1 | NM_138381.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251296Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135808
GnomAD4 exome AF: 0.000127 AC: 186AN: 1461750Hom.: 0 Cov.: 31 AF XY: 0.000128 AC XY: 93AN XY: 727184
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2023 | The c.844A>C (p.I282L) alteration is located in exon 9 (coding exon 7) of the OXNAD1 gene. This alteration results from a A to C substitution at nucleotide position 844, causing the isoleucine (I) at amino acid position 282 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