18-9886934-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032243.6(TXNDC2):c.254C>T(p.Ser85Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032243.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TXNDC2 | NM_032243.6 | c.254C>T | p.Ser85Phe | missense_variant | Exon 2 of 2 | ENST00000357775.6 | NP_115619.4 | |
TXNDC2 | NM_001098529.2 | c.455C>T | p.Ser152Phe | missense_variant | Exon 2 of 2 | NP_001091999.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151848Hom.: 0 Cov.: 30
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461502Hom.: 0 Cov.: 116 AF XY: 0.00 AC XY: 0AN XY: 727058
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151848Hom.: 0 Cov.: 30 AF XY: 0.0000539 AC XY: 4AN XY: 74144
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.455C>T (p.S152F) alteration is located in exon 2 (coding exon 2) of the TXNDC2 gene. This alteration results from a C to T substitution at nucleotide position 455, causing the serine (S) at amino acid position 152 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at