rs604229
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022463.5(NXN):c.361-57510G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,272 control chromosomes in the GnomAD database, including 1,300 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 0.12 ( 1300 hom., cov: 33)
Consequence
NXN
NM_022463.5 intron
NM_022463.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.498
Genes affected
NXN (HGNC:18008): (nucleoredoxin) This gene encodes a member of the thioredoxin superfamily, a group of small, multifunctional redox-active proteins. Members of this family are characterized by a conserved active motif called the thioredoxin fold that catalyzes disulfide bond formation and isomerization. The encoded protein acts a redox-dependent regulator of the Wnt signaling pathway and is involved in cell growth and differentiation. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NXN | NM_022463.5 | c.361-57510G>A | intron_variant | ENST00000336868.8 | |||
NXN | XM_005256756.5 | c.361-57510G>A | intron_variant | ||||
NXN | XM_005256758.4 | c.21+13298G>A | intron_variant | ||||
NXN | XM_017024949.2 | c.361-57510G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NXN | ENST00000336868.8 | c.361-57510G>A | intron_variant | 1 | NM_022463.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.122 AC: 18508AN: 152154Hom.: 1302 Cov.: 33
GnomAD3 genomes
?
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152154
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.121 AC: 18496AN: 152272Hom.: 1300 Cov.: 33 AF XY: 0.127 AC XY: 9426AN XY: 74456
GnomAD4 genome
?
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18496
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152272
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33
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9426
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74456
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649
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at