8-30679706-CTT-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000637.5(GSR):c.1420-39_1420-38delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 1,213,742 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0020 ( 1 hom., cov: 0)
Exomes 𝑓: 0.14 ( 0 hom. )
Consequence
GSR
NM_000637.5 intron
NM_000637.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.48
Genes affected
GSR (HGNC:4623): (glutathione-disulfide reductase) This gene encodes a member of the class-I pyridine nucleotide-disulfide oxidoreductase family. This enzyme is a homodimeric flavoprotein. It is a central enzyme of cellular antioxidant defense, and reduces oxidized glutathione disulfide (GSSG) to the sulfhydryl form GSH, which is an important cellular antioxidant. Rare mutations in this gene result in hereditary glutathione reductase deficiency. Multiple alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 8-30679706-CTT-C is Benign according to our data. Variant chr8-30679706-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1286961.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSR | NM_000637.5 | c.1420-39_1420-38delAA | intron_variant | ENST00000221130.11 | NP_000628.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSR | ENST00000221130.11 | c.1420-39_1420-38delAA | intron_variant | 1 | NM_000637.5 | ENSP00000221130.5 |
Frequencies
GnomAD3 genomes AF: 0.00203 AC: 274AN: 134800Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.183 AC: 24102AN: 131578Hom.: 0 AF XY: 0.185 AC XY: 13402AN XY: 72352
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GnomAD4 exome AF: 0.137 AC: 148300AN: 1078942Hom.: 0 AF XY: 0.138 AC XY: 74381AN XY: 538252
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GnomAD4 genome AF: 0.00204 AC: 275AN: 134800Hom.: 1 Cov.: 0 AF XY: 0.00239 AC XY: 155AN XY: 64878
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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 | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at