rs116054286
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006440.5(TXNRD2):c.529-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000912 in 1,612,912 control chromosomes in the GnomAD database, including 14 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 Likely benign (★★).
Frequency
Consequence
NM_006440.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNRD2 | NM_006440.5 | c.529-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000400521.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNRD2 | ENST00000400521.7 | c.529-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006440.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00484 AC: 736AN: 152160Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00115 AC: 283AN: 246100Hom.: 0 AF XY: 0.000824 AC XY: 110AN XY: 133524
GnomAD4 exome AF: 0.000502 AC: 733AN: 1460634Hom.: 8 Cov.: 31 AF XY: 0.000427 AC XY: 310AN XY: 726378
GnomAD4 genome ? AF: 0.00485 AC: 738AN: 152278Hom.: 6 Cov.: 32 AF XY: 0.00418 AC XY: 311AN XY: 74460
ClinVar
Submissions by phenotype
Glucocorticoid deficiency 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 02, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Primary dilated cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at