chr3-126621755-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_052883.3(TXNRD3):c.1511C>T(p.Ala504Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000147 in 1,358,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052883.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNRD3 | NM_052883.3 | c.1511C>T | p.Ala504Val | missense_variant | 12/16 | ENST00000524230.9 | |
TXNRD3 | NM_001173513.3 | c.1511C>T | p.Ala504Val | missense_variant | 12/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNRD3 | ENST00000524230.9 | c.1511C>T | p.Ala504Val | missense_variant | 12/16 | 1 | NM_052883.3 | P1 | |
TXNRD3 | ENST00000523403.3 | c.1511C>T | p.Ala504Val | missense_variant | 12/15 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000147 AC: 2AN: 1358784Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 670068
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2021 | The c.1511C>T (p.A504V) alteration is located in exon 12 (coding exon 12) of the TXNRD3 gene. This alteration results from a C to T substitution at nucleotide position 1511, causing the alanine (A) at amino acid position 504 to be replaced by a valine (V). 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