rs2281843

Variant names:

• chr10-130181652-T-C
• rs2281843
• ENST00000481034.1:n.*237+1331T>C

Variant summary

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

The ENST00000481034.1(GLRX3):​n.*237+1331T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 152,232 control chromosomes in the GnomAD database, including 535 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 0.057 (535 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GLRX3 ENST00000481034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473
• Publications: 1 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 = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902561	XM_047426136.1	c.-6201+1331T>C		intron_variant	Intron 1 of 1		XP_047282092.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLRX3	ENST00000481034.1	n.*237+1331T>C		intron_variant	Intron 12 of 12	1		ENSP00000435445.1
GLRX3	ENST00000368644.5	c.*1568T>C		3_prime_UTR_variant	Exon 12 of 12	2		ENSP00000357633.1
GLRX3	ENST00000619341.1	n.137+1331T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0566 AC: 8614 AN: 152114 Hom.: 533 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0625

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.0206

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00716

Gnomad OTH AF: 0.0531

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

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: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0567 AC: 8634 AN: 152232 Hom.: 535 Cov.: 33 AF XY: 0.0565 AC XY: 4202 AN XY: 74434

African (AFR) AF: 0.147 AC: 6111 AN: 41522

American (AMR) AF: 0.0625 AC: 955 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.100 AC: 519 AN: 5176

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4818

European-Finnish (FIN) AF: 0.0206 AC: 219 AN: 10606

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00716 AC: 487 AN: 68032

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0396 Hom.: 44

Bravo AF: 0.0653

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.69
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2281843; hg19: chr10-131979916;