chr10-130180094-A-G

Variant names:

• chr10-130180094-A-G
• rs3750834
• ENST00000481034.1:n.*29-19A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000481034.1(GLRX3):​n.*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 ENST00000481034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 6 publications found

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]

LOC124902561 (HGNC:):

ACMG classification

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: ENST00000481034.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLRX3	ENST00000481034.1	TSL:1	n.*29-19A>G		intron	N/A	ENSP00000435445.1
	GLRX3	ENST00000368644.5	TSL:2	c.*29-19A>G		intron	N/A	ENSP00000357633.1
	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.: 30

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: 21 AN: 80 Hom.: 7 Cov.: 0 AF XY: 0.250 AC XY: 16 AN XY: 64

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.125 AC: 1 AN: 8

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.294 AC: 20 AN: 68

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.443 AC: 58160 AN: 131284 Hom.: 12913 Cov.: 30 AF XY: 0.445 AC XY: 28166 AN XY: 63244

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

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
DANN	Benign	0.61
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3750834; hg19: chr10-131978358;