rs2251780
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000637.5(GSR):c.306+124C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 931,240 control chromosomes in the GnomAD database, including 16,435 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.20 ( 3230 hom., cov: 32)
Exomes 𝑓: 0.18 ( 13205 hom. )
Consequence
GSR
NM_000637.5 intron
NM_000637.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.24
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 8-30727406-G-A is Benign according to our data. Variant chr8-30727406-G-A is described in ClinVar as [Benign]. Clinvar id is 1288174.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSR | NM_000637.5 | c.306+124C>T | intron_variant | ENST00000221130.11 | NP_000628.2 | |||
GSR | NM_001195102.3 | c.306+124C>T | intron_variant | NP_001182031.1 | ||||
GSR | NM_001195103.3 | c.306+124C>T | intron_variant | NP_001182032.1 | ||||
GSR | NM_001195104.3 | c.306+124C>T | intron_variant | NP_001182033.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSR | ENST00000221130.11 | c.306+124C>T | intron_variant | 1 | NM_000637.5 | ENSP00000221130 | P1 |
Frequencies
GnomAD3 genomes AF: 0.200 AC: 30327AN: 152014Hom.: 3220 Cov.: 32
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GnomAD4 exome AF: 0.176 AC: 137153AN: 779108Hom.: 13205 AF XY: 0.181 AC XY: 71992AN XY: 397498
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GnomAD4 genome AF: 0.200 AC: 30372AN: 152132Hom.: 3230 Cov.: 32 AF XY: 0.202 AC XY: 15034AN XY: 74364
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
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