NM_052883.3:c.1367+23A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_052883.3(TXNRD3):c.1367+23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 1,505,454 control chromosomes in the GnomAD database, including 4,247 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 0.073 ( 468 hom., cov: 32)
Exomes 𝑓: 0.069 ( 3779 hom. )
Consequence
TXNRD3
NM_052883.3 intron
NM_052883.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.923
Publications
7 publications found
Genes affected
TXNRD3 (HGNC:20667): (thioredoxin reductase 3) The protein encoded by this gene belongs to the pyridine nucleotide-disulfide oxidoreductase family, and is a member of the thioredoxin (Trx) system. Three thioredoxin reductase (TrxR) isozymes are found in mammals. TrxRs are selenocysteine-containing flavoenzymes, which reduce thioredoxins, as well as other substrates, and play a key role in redox homoeostasis. This gene encodes the third TrxR, which unlike the other two isozymes, contains an additional N-terminal glutaredoxin (Grx) domain, and shows highest expression in testis. The Grx domain allows this isozyme to participate in both Trx and glutathione systems. It functions as a homodimer containing FAD, and selenocysteine (Sec) at the active site. Sec is encoded by UGA codon that normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, the Sec insertion sequence (SECIS) element, which is necessary for the recognition of UGA as a Sec codon rather than as a stop signal. Alternatively spliced transcript variants have been found for this gene. Experimental evidence suggests the use of a non-AUG (CUG) codon as a translation initiation codon (PMID:20018845). [provided by RefSeq, Aug 2017]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0730 AC: 11105AN: 152128Hom.: 463 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
11105
AN:
152128
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0861 AC: 11218AN: 130328 AF XY: 0.0856 show subpopulations
GnomAD2 exomes
AF:
AC:
11218
AN:
130328
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0694 AC: 93851AN: 1353208Hom.: 3779 Cov.: 24 AF XY: 0.0700 AC XY: 46857AN XY: 669192 show subpopulations
GnomAD4 exome
AF:
AC:
93851
AN:
1353208
Hom.:
Cov.:
24
AF XY:
AC XY:
46857
AN XY:
669192
show subpopulations
African (AFR)
AF:
AC:
1775
AN:
30710
American (AMR)
AF:
AC:
3210
AN:
33566
Ashkenazi Jewish (ASJ)
AF:
AC:
1769
AN:
24706
East Asian (EAS)
AF:
AC:
6602
AN:
35488
South Asian (SAS)
AF:
AC:
6574
AN:
76928
European-Finnish (FIN)
AF:
AC:
3023
AN:
33768
Middle Eastern (MID)
AF:
AC:
344
AN:
5610
European-Non Finnish (NFE)
AF:
AC:
66395
AN:
1055608
Other (OTH)
AF:
AC:
4159
AN:
56824
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
4058
8116
12173
16231
20289
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2486
4972
7458
9944
12430
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0731 AC: 11126AN: 152246Hom.: 468 Cov.: 32 AF XY: 0.0745 AC XY: 5547AN XY: 74436 show subpopulations
GnomAD4 genome
AF:
AC:
11126
AN:
152246
Hom.:
Cov.:
32
AF XY:
AC XY:
5547
AN XY:
74436
show subpopulations
African (AFR)
AF:
AC:
2498
AN:
41548
American (AMR)
AF:
AC:
1300
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
269
AN:
3468
East Asian (EAS)
AF:
AC:
1019
AN:
5166
South Asian (SAS)
AF:
AC:
420
AN:
4826
European-Finnish (FIN)
AF:
AC:
895
AN:
10614
Middle Eastern (MID)
AF:
AC:
18
AN:
294
European-Non Finnish (NFE)
AF:
AC:
4526
AN:
68014
Other (OTH)
AF:
AC:
157
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
526
1052
1579
2105
2631
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
138
276
414
552
690
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
520
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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