15-69026607-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024505.4(NOX5):c.130G>A(p.Glu44Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000178 in 1,614,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024505.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOX5 | NM_024505.4 | c.130G>A | p.Glu44Lys | missense_variant | 2/16 | ENST00000388866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOX5 | ENST00000388866.8 | c.130G>A | p.Glu44Lys | missense_variant | 2/16 | 1 | NM_024505.4 | ||
NOX5 | ENST00000530406.7 | c.130G>A | p.Glu44Lys | missense_variant | 2/16 | 1 | P1 | ||
NOX5 | ENST00000527315.5 | n.134G>A | non_coding_transcript_exon_variant | 2/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 162AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000215 AC: 54AN: 251456Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135900
GnomAD4 exome AF: 0.0000841 AC: 123AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727232
GnomAD4 genome AF: 0.00108 AC: 164AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.00110 AC XY: 82AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at