chr15-69035845-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024505.4(NOX5):c.1097C>T(p.Ser366Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,614,046 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_024505.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOX5 | NM_024505.4 | c.1097C>T | p.Ser366Leu | missense_variant | 7/16 | ENST00000388866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOX5 | ENST00000388866.8 | c.1097C>T | p.Ser366Leu | missense_variant | 7/16 | 1 | NM_024505.4 | ||
NOX5 | ENST00000530406.7 | c.1013C>T | p.Ser338Leu | missense_variant | 7/16 | 1 | P1 | ||
NOX5 | ENST00000525143.5 | c.497C>T | p.Ser166Leu | missense_variant, NMD_transcript_variant | 4/12 | 1 | |||
NOX5 | ENST00000527315.5 | n.4253C>T | non_coding_transcript_exon_variant | 6/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251436Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135892
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461870Hom.: 0 Cov.: 40 AF XY: 0.0000481 AC XY: 35AN XY: 727236
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.1097C>T (p.S366L) alteration is located in exon 7 (coding exon 7) of the NOX5 gene. This alteration results from a C to T substitution at nucleotide position 1097, causing the serine (S) at amino acid position 366 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