chr10-130166520-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_006541.5(GLRX3):c.492G>A(p.Gln164=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0093 in 1,612,948 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0081 ( 11 hom., cov: 32)
Exomes 𝑓: 0.0094 ( 121 hom. )
Consequence
GLRX3
NM_006541.5 synonymous
NM_006541.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.67
Genes affected
GLRX3 (HGNC:15987): (glutaredoxin 3) This gene encodes a member of the glutaredoxin family. Glutaredoxins are oxidoreductase enzymes that reduce a variety of substrates using glutathione as a cofactor. The encoded protein binds to and modulates the function of protein kinase C theta. The encoded protein may also inhibit apoptosis and play a role in cellular growth, and the expression of this gene may be a marker for cancer. Pseudogenes of this gene are located on the short arm of chromosomes 6 and 9. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 10-130166520-G-A is Benign according to our data. Variant chr10-130166520-G-A is described in ClinVar as [Benign]. Clinvar id is 771743.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.66 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00943 (13775/1460664) while in subpopulation MID AF= 0.0188 (108/5752). AF 95% confidence interval is 0.0159. There are 121 homozygotes in gnomad4_exome. There are 6969 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRX3 | NM_006541.5 | c.492G>A | p.Gln164= | synonymous_variant | 5/11 | ENST00000331244.10 | |
GLRX3 | NM_001199868.2 | c.492G>A | p.Gln164= | synonymous_variant | 5/12 | ||
GLRX3 | NM_001321980.2 | c.54G>A | p.Gln18= | synonymous_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRX3 | ENST00000331244.10 | c.492G>A | p.Gln164= | synonymous_variant | 5/11 | 1 | NM_006541.5 | P1 | |
GLRX3 | ENST00000481034.1 | c.492G>A | p.Gln164= | synonymous_variant, NMD_transcript_variant | 5/13 | 1 | |||
GLRX3 | ENST00000368644.5 | c.492G>A | p.Gln164= | synonymous_variant | 5/12 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00810 AC: 1233AN: 152166Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00959 AC: 2405AN: 250738Hom.: 31 AF XY: 0.00987 AC XY: 1338AN XY: 135534
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GnomAD4 exome AF: 0.00943 AC: 13775AN: 1460664Hom.: 121 Cov.: 29 AF XY: 0.00959 AC XY: 6969AN XY: 726670
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GnomAD4 genome ? AF: 0.00809 AC: 1232AN: 152284Hom.: 11 Cov.: 32 AF XY: 0.00743 AC XY: 553AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at