rs180876844
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_006440.5(TXNRD2):c.375-8C>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 0.000441 in 1,613,994 control chromosomes in the GnomAD database, including 2 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
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNRD2 | NM_006440.5 | c.375-8C>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.375-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006440.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000427 AC: 65AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000477 AC: 119AN: 249462Hom.: 0 AF XY: 0.000510 AC XY: 69AN XY: 135360
GnomAD4 exome AF: 0.000442 AC: 646AN: 1461628Hom.: 2 Cov.: 31 AF XY: 0.000484 AC XY: 352AN XY: 727134
GnomAD4 genome ? AF: 0.000427 AC: 65AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 06, 2020 | This variant is associated with the following publications: (PMID: 26656175) - |
Primary dilated cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at