chr22-36467825-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_012473.4(TXN2):c.480C>T(p.Phe160=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000684 in 1,461,638 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: not found (cov: 33)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
TXN2
NM_012473.4 synonymous
NM_012473.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.79
Genes affected
TXN2 (HGNC:17772): (thioredoxin 2) This nuclear gene encodes a mitochondrial member of the thioredoxin family, a group of small multifunctional redox-active proteins. The encoded protein may play important roles in the regulation of the mitochondrial membrane potential and in protection against oxidant-induced apoptosis. [provided by RefSeq, Jul 2008]
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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=-0.38).
BP6
Variant 22-36467825-G-A is Benign according to our data. Variant chr22-36467825-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1962579.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXN2 | NM_012473.4 | c.480C>T | p.Phe160= | synonymous_variant | 4/4 | ENST00000216185.7 | |
TXN2 | XM_006724226.2 | c.480C>T | p.Phe160= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXN2 | ENST00000216185.7 | c.480C>T | p.Phe160= | synonymous_variant | 4/4 | 1 | NM_012473.4 | P1 | |
TXN2 | ENST00000403313.5 | c.480C>T | p.Phe160= | synonymous_variant | 4/4 | 3 | P1 | ||
TXN2 | ENST00000416967.1 | c.174C>T | p.Phe58= | synonymous_variant | 4/4 | 2 | |||
TXN2 | ENST00000487725.1 | n.460C>T | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249382Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134972
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461638Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727132
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GnomAD4 genome Cov.: 33
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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 | May 08, 2023 | - - |
Computational scores
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Name
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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