17-801102-G-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_022463.5(NXN):c.1155C>T(p.Tyr385Tyr) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000352 in 1,562,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
NXN
NM_022463.5 synonymous
NM_022463.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.82
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 17-801102-G-A is Benign according to our data. Variant chr17-801102-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1986198.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NXN | NM_022463.5 | c.1155C>T | p.Tyr385Tyr | synonymous_variant | 8/8 | ENST00000336868.8 | NP_071908.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NXN | ENST00000336868.8 | c.1155C>T | p.Tyr385Tyr | synonymous_variant | 8/8 | 1 | NM_022463.5 | ENSP00000337443.3 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152094Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000374 AC: 8AN: 213736Hom.: 0 AF XY: 0.0000172 AC XY: 2AN XY: 116456
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GnomAD4 exome AF: 0.0000206 AC: 29AN: 1410684Hom.: 0 Cov.: 31 AF XY: 0.0000186 AC XY: 13AN XY: 699686
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GnomAD4 genome AF: 0.000171 AC: 26AN: 152094Hom.: 0 Cov.: 31 AF XY: 0.000215 AC XY: 16AN XY: 74318
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 04, 2022 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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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