chr22-36467836-A-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_012473.4(TXN2):āc.469T>Cā(p.Leu157=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000285 in 1,614,072 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 (ā ).
Frequency
Genomes: š 0.000066 ( 0 hom., cov: 33)
Exomes š: 0.000025 ( 0 hom. )
Consequence
TXN2
NM_012473.4 synonymous
NM_012473.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.39
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 -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 22-36467836-A-G is Benign according to our data. Variant chr22-36467836-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 756285.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.469T>C | p.Leu157= | synonymous_variant | 4/4 | ENST00000216185.7 | |
TXN2 | XM_006724226.2 | c.469T>C | p.Leu157= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXN2 | ENST00000216185.7 | c.469T>C | p.Leu157= | synonymous_variant | 4/4 | 1 | NM_012473.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152268Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249310Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 134944
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GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461804Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727204
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74394
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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 | Dec 31, 2019 | - - |
Computational scores
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Benign
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at