14-52432583-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020784.3(TXNDC16):c.2199T>G(p.Ile733Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000344 in 1,600,304 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC16 | NM_020784.3 | c.2199T>G | p.Ile733Met | missense_variant | 21/21 | ENST00000281741.9 | |
TXNDC16 | NM_001160047.2 | c.2184T>G | p.Ile728Met | missense_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.2199T>G | p.Ile733Met | missense_variant | 21/21 | 1 | NM_020784.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000292 AC: 7AN: 239524Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129684
GnomAD4 exome AF: 0.0000318 AC: 46AN: 1448108Hom.: 0 Cov.: 31 AF XY: 0.0000361 AC XY: 26AN XY: 719424
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | The c.2199T>G (p.I733M) alteration is located in exon 21 (coding exon 19) of the TXNDC16 gene. This alteration results from a T to G substitution at nucleotide position 2199, causing the isoleucine (I) at amino acid position 733 to be replaced by a methionine (M). 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