10-130145269-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006541.5(GLRX3):c.151G>A(p.Glu51Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000101 in 1,580,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006541.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRX3 | NM_006541.5 | c.151G>A | p.Glu51Lys | missense_variant | 2/11 | ENST00000331244.10 | |
GLRX3 | NM_001199868.2 | c.151G>A | p.Glu51Lys | missense_variant | 2/12 | ||
GLRX3 | NM_001321980.2 | c.-377G>A | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRX3 | ENST00000331244.10 | c.151G>A | p.Glu51Lys | missense_variant | 2/11 | 1 | NM_006541.5 | P1 | |
GLRX3 | ENST00000481034.1 | c.151G>A | p.Glu51Lys | missense_variant, NMD_transcript_variant | 2/13 | 1 | |||
GLRX3 | ENST00000368644.5 | c.151G>A | p.Glu51Lys | missense_variant | 2/12 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251248Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135804
GnomAD4 exome AF: 0.0000105 AC: 15AN: 1427768Hom.: 0 Cov.: 24 AF XY: 0.0000112 AC XY: 8AN XY: 712206
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.151G>A (p.E51K) alteration is located in exon 2 (coding exon 2) of the GLRX3 gene. This alteration results from a G to A substitution at nucleotide position 151, causing the glutamic acid (E) at amino acid position 51 to be replaced by a lysine (K). 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