14-52482863-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020784.3(TXNDC16):c.1211C>T(p.Thr404Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,612,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020784.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC16 | NM_020784.3 | c.1211C>T | p.Thr404Ile | missense_variant | 13/21 | ENST00000281741.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.1211C>T | p.Thr404Ile | missense_variant | 13/21 | 1 | NM_020784.3 | P1 | |
TXNDC16 | ENST00000554399.1 | n.208-42139C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 250120Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135314
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459906Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726332
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 21, 2022 | The c.1211C>T (p.T404I) alteration is located in exon 13 (coding exon 11) of the TXNDC16 gene. This alteration results from a C to T substitution at nucleotide position 1211, causing the threonine (T) at amino acid position 404 to be replaced by an isoleucine (I). 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