Genetic Variant GLRX3:n.*29-19A>G (chr10-130180094-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001199868.2(GLRX3):c.*29-19A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 131,364 control chromosomes in the GnomAD database, including 12,920 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 12913 hom., cov: 30)

Exomes 𝑓: 0.26 ( 7 hom. )

Consequence

GLRX3
NM_001199868.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

Publications

6 publications found

Variant links:

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]

GLRX3 links:

LOC124902561 (HGNC:):

LOC124902561 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199868.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLRX3	NM_001199868.2		c.*29-19A>G		intron	N/A	NP_001186797.1	O76003

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GLRX3	ENST00000481034.1	TSL:1	n.*29-19A>G	intron	N/A	ENSP00000435445.1	O76003
GLRX3	ENST00000368644.5	TSL:2	c.*29-19A>G	intron	N/A	ENSP00000357633.1	O76003
GLRX3	ENST00000496195.1	TSL:2	n.48-19A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

58097

AN:

131204

Hom.:

12891

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.394

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.448

GnomAD4 exome

AF:

0.263

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.125

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.294

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.443

AC:

58160

AN:

131284

Hom.:

12913

Cov.:

AF XY:

0.445

AC XY:

28166

AN XY:

63244

show subpopulations

African (AFR)

AF:

0.664

AC:

25045

AN:

37714

American (AMR)

AF:

0.472

AC:

6269

AN:

13292

Ashkenazi Jewish (ASJ)

AF:

0.298

AC:

833

AN:

2794

East Asian (EAS)

AF:

0.352

AC:

1671

AN:

4742

South Asian (SAS)

AF:

0.210

AC:

717

AN:

3414

European-Finnish (FIN)

AF:

0.365

AC:

2896

AN:

7938

Middle Eastern (MID)

AF:

0.466

AC:

110

AN:

236

European-Non Finnish (NFE)

AF:

0.333

AC:

19525

AN:

58614

Other (OTH)

AF:

0.448

AC:

777

AN:

1736

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1617

3233

4850

6466

8083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.318

Hom.:

20272

Bravo

AF:

0.412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.012

(source)

DANN

Benign

0.61

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over