NM_006541.5:c.479-1119T>C

Variant names:

• chr10-130165388-T-C
• rs11017114
• NM_006541.5:c.479-1119T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_006541.5(GLRX3):​c.479-1119T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,124 control chromosomes in the GnomAD database, including 530 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 0.072 (530 hom., cov: 33)
• Consequence: GLRX3 NM_006541.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006541.5. 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_006541.5	MANE Select	c.479-1119T>C		intron	N/A	NP_006532.2	A0A140VJK1
	GLRX3	NM_001199868.2		c.479-1119T>C		intron	N/A	NP_001186797.1	O76003
	GLRX3	NM_001321980.2		c.41-1119T>C		intron	N/A	NP_001308909.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLRX3	ENST00000331244.10	TSL:1 MANE Select	c.479-1119T>C		intron	N/A	ENSP00000330836.5	O76003
	GLRX3	ENST00000481034.1	TSL:1	n.479-1119T>C		intron	N/A	ENSP00000435445.1	O76003
	GLRX3	ENST00000861475.1		c.572-1119T>C		intron	N/A	ENSP00000531534.1

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10956 AN: 152004 Hom.: 529 Cov.: 33

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0760

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0830

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0721 AC: 10966 AN: 152124 Hom.: 530 Cov.: 33 AF XY: 0.0697 AC XY: 5185 AN XY: 74384

African (AFR) AF: 0.0188 AC: 781 AN: 41462

American (AMR) AF: 0.0760 AC: 1162 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3470

East Asian (EAS) AF: 0.0148 AC: 77 AN: 5188

South Asian (SAS) AF: 0.0697 AC: 336 AN: 4824

European-Finnish (FIN) AF: 0.0556 AC: 589 AN: 10600

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7300 AN: 67982

Other (OTH) AF: 0.0840 AC: 177 AN: 2106

Alfa AF: 0.0645 Hom.: 136

Bravo AF: 0.0720

Asia WGS AF: 0.0550 AC: 191 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11017114; hg19: chr10-131963652;