rs35695986
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006440.5(TXNRD2):c.903C>T(p.Thr301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,613,936 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T301T) has been classified as Benign.
Frequency
Consequence
NM_006440.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNRD2 | NM_006440.5 | c.903C>T | p.Thr301= | synonymous_variant | 11/18 | ENST00000400521.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNRD2 | ENST00000400521.7 | c.903C>T | p.Thr301= | synonymous_variant | 11/18 | 1 | NM_006440.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000924 AC: 23AN: 249044Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135128
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461604Hom.: 0 Cov.: 33 AF XY: 0.0000591 AC XY: 43AN XY: 727090
GnomAD4 genome AF: 0.000210 AC: 32AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 01, 2020 | - - |
Primary dilated cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2016 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at