chr15-69033137-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_024505.4(NOX5):c.715C>A(p.Leu239Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,569,486 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOX5 | NM_024505.4 | c.715C>A | p.Leu239Met | missense_variant | 5/16 | ENST00000388866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOX5 | ENST00000388866.8 | c.715C>A | p.Leu239Met | missense_variant | 5/16 | 1 | NM_024505.4 | ||
NOX5 | ENST00000530406.7 | c.631C>A | p.Leu211Met | missense_variant | 5/16 | 1 | P1 | ||
NOX5 | ENST00000525143.5 | c.115C>A | p.Leu39Met | missense_variant, NMD_transcript_variant | 2/12 | 1 | |||
NOX5 | ENST00000527315.5 | n.3871C>A | non_coding_transcript_exon_variant | 4/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000270 AC: 5AN: 184876Hom.: 0 AF XY: 0.0000397 AC XY: 4AN XY: 100860
GnomAD4 exome AF: 0.000116 AC: 164AN: 1417282Hom.: 2 Cov.: 33 AF XY: 0.000102 AC XY: 72AN XY: 702458
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.715C>A (p.L239M) alteration is located in exon 5 (coding exon 5) of the NOX5 gene. This alteration results from a C to A substitution at nucleotide position 715, causing the leucine (L) at amino acid position 239 to be replaced by a methionine (M). 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