rs61736929
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006440.5(TXNRD2):āc.526G>Cā(p.Glu176Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00408 in 1,614,186 control chromosomes in the GnomAD database, including 252 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_006440.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TXNRD2 | NM_006440.5 | c.526G>C | p.Glu176Gln | missense_variant, splice_region_variant | 6/18 | ENST00000400521.7 | NP_006431.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TXNRD2 | ENST00000400521.7 | c.526G>C | p.Glu176Gln | missense_variant, splice_region_variant | 6/18 | 1 | NM_006440.5 | ENSP00000383365.1 |
Frequencies
GnomAD3 genomes AF: 0.0218 AC: 3323AN: 152198Hom.: 120 Cov.: 32
GnomAD3 exomes AF: 0.00547 AC: 1364AN: 249576Hom.: 51 AF XY: 0.00416 AC XY: 563AN XY: 135410
GnomAD4 exome AF: 0.00221 AC: 3230AN: 1461870Hom.: 128 Cov.: 31 AF XY: 0.00194 AC XY: 1410AN XY: 727236
GnomAD4 genome AF: 0.0220 AC: 3348AN: 152316Hom.: 124 Cov.: 32 AF XY: 0.0208 AC XY: 1553AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 19, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Primary dilated cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 25, 2015 | This alteration is classified as 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