chr22-36476776-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012473.4(TXN2):āc.344A>Gā(p.Lys115Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000805 in 1,614,086 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. K115K) has been classified as Likely benign.
Frequency
Consequence
NM_012473.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXN2 | NM_012473.4 | c.344A>G | p.Lys115Arg | missense_variant | 3/4 | ENST00000216185.7 | |
TXN2 | XM_006724226.2 | c.344A>G | p.Lys115Arg | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXN2 | ENST00000216185.7 | c.344A>G | p.Lys115Arg | missense_variant | 3/4 | 1 | NM_012473.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251490Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135918
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461890Hom.: 0 Cov.: 33 AF XY: 0.0000853 AC XY: 62AN XY: 727248
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2023 | The c.344A>G (p.K115R) alteration is located in exon 3 (coding exon 2) of the TXN2 gene. This alteration results from a A to G substitution at nucleotide position 344, causing the lysine (K) at amino acid position 115 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at