rs11017114

Positions:

• chr10-130165388-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLRX3	NM_006541.5	c.479-1119T>C		intron_variant		ENST00000331244.10	NP_006532.2
GLRX3	NM_001199868.2	c.479-1119T>C		intron_variant			NP_001186797.1
GLRX3	NM_001321980.2	c.41-1119T>C		intron_variant			NP_001308909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLRX3	ENST00000331244.10	c.479-1119T>C		intron_variant		1	NM_006541.5	ENSP00000330836	P1
GLRX3	ENST00000481034.1	c.479-1119T>C		intron_variant, NMD_transcript_variant		1		ENSP00000435445
GLRX3	ENST00000368644.5	c.479-1119T>C		intron_variant		2		ENSP00000357633	P1

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

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0760

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0148

Gnomad4 SAS AF: 0.0697

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0840

Alfa AF: 0.0822 Hom.: 115

Bravo AF: 0.0720

Asia WGS AF: 0.0550 AC: 191 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs11017114; hg19: chr10-131963652;