chr10-130145239-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006541.5(GLRX3):c.121C>T(p.Pro41Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,523,774 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 Uncertain significance (★).
Frequency
Consequence
NM_006541.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRX3 | NM_006541.5 | c.121C>T | p.Pro41Ser | missense_variant | 2/11 | ENST00000331244.10 | |
GLRX3 | NM_001199868.2 | c.121C>T | p.Pro41Ser | missense_variant | 2/12 | ||
GLRX3 | NM_001321980.2 | c.-407C>T | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRX3 | ENST00000331244.10 | c.121C>T | p.Pro41Ser | missense_variant | 2/11 | 1 | NM_006541.5 | P1 | |
GLRX3 | ENST00000481034.1 | c.121C>T | p.Pro41Ser | missense_variant, NMD_transcript_variant | 2/13 | 1 | |||
GLRX3 | ENST00000368644.5 | c.121C>T | p.Pro41Ser | missense_variant | 2/12 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152066Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247592Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133950
GnomAD4 exome AF: 0.0000146 AC: 20AN: 1371708Hom.: 0 Cov.: 23 AF XY: 0.0000161 AC XY: 11AN XY: 682668
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152066Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.121C>T (p.P41S) alteration is located in exon 2 (coding exon 2) of the GLRX3 gene. This alteration results from a C to T substitution at nucleotide position 121, causing the proline (P) at amino acid position 41 to be replaced by a serine (S). 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