rs13991

Variant names:

• chr10-130136483-G-A
• rs13991
• NM_006541.5:c.63G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-130136483-G-A
• chr10-130136483-G-C
• chr10-130136483-G-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_006541.5(GLRX3):​c.63G>A​(p.Gln21Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GLRX3 NM_006541.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.640
• Publications: 16 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]

ENSG00000300559 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BP7: Synonymous conserved (PhyloP=0.64 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLRX3	NM_006541.5	c.63G>A	p.Gln21Gln	synonymous_variant	Exon 1 of 11	ENST00000331244.10	NP_006532.2
GLRX3	NM_001199868.2	c.63G>A	p.Gln21Gln	synonymous_variant	Exon 1 of 12		NP_001186797.1
GLRX3	NM_001321980.2	c.-465G>A		5_prime_UTR_variant	Exon 1 of 12		NP_001308909.1
LOC105378561	XR_001747659.2	n.-112C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLRX3	ENST00000331244.10	c.63G>A	p.Gln21Gln	synonymous_variant	Exon 1 of 11	1	NM_006541.5	ENSP00000330836.5
GLRX3	ENST00000481034.1	n.63G>A		non_coding_transcript_exon_variant	Exon 1 of 13	1		ENSP00000435445.1
GLRX3	ENST00000368644.5	c.63G>A	p.Gln21Gln	synonymous_variant	Exon 1 of 12	2		ENSP00000357633.1
ENSG00000300559	ENST00000772722.1	n.-153C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1114200 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 530060

African (AFR) AF: 0.00 AC: 0 AN: 23232

American (AMR) AF: 0.00 AC: 0 AN: 9512

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14844

East Asian (EAS) AF: 0.00 AC: 0 AN: 26818

South Asian (SAS) AF: 0.00 AC: 0 AN: 24258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36104

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2986

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 931922

Other (OTH) AF: 0.00 AC: 0 AN: 44524

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	12
DANN	Benign	0.96
PhyloP100		0.64
PromoterAI		-0.0067	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs13991; hg19: chr10-131934747;