chr10-130169440-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006541.5(GLRX3):c.721G>T(p.Val241Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,609,090 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRX3 | NM_006541.5 | c.721G>T | p.Val241Leu | missense_variant | 7/11 | ENST00000331244.10 | |
GLRX3 | NM_001199868.2 | c.721G>T | p.Val241Leu | missense_variant | 7/12 | ||
GLRX3 | NM_001321980.2 | c.283G>T | p.Val95Leu | missense_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRX3 | ENST00000331244.10 | c.721G>T | p.Val241Leu | missense_variant | 7/11 | 1 | NM_006541.5 | P1 | |
GLRX3 | ENST00000481034.1 | c.721G>T | p.Val241Leu | missense_variant, NMD_transcript_variant | 7/13 | 1 | |||
GLRX3 | ENST00000368644.5 | c.721G>T | p.Val241Leu | missense_variant | 7/12 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251378Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135874
GnomAD4 exome AF: 0.0000426 AC: 62AN: 1456896Hom.: 0 Cov.: 28 AF XY: 0.0000524 AC XY: 38AN XY: 725240
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.721G>T (p.V241L) alteration is located in exon 7 (coding exon 7) of the GLRX3 gene. This alteration results from a G to T substitution at nucleotide position 721, causing the valine (V) at amino acid position 241 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