12-104288936-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001093771.3(TXNRD1):c.310G>A(p.Gly104Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001093771.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNRD1 | NM_001093771.3 | c.310G>A | p.Gly104Ser | missense_variant | 4/17 | ENST00000525566.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNRD1 | ENST00000525566.6 | c.310G>A | p.Gly104Ser | missense_variant | 4/17 | 1 | NM_001093771.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000709 AC: 108AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000193 AC: 48AN: 249284Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135246
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461696Hom.: 0 Cov.: 30 AF XY: 0.0000729 AC XY: 53AN XY: 727124
GnomAD4 genome AF: 0.000709 AC: 108AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.000792 AC XY: 59AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at