14-52482894-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020784.3(TXNDC16):c.1180G>C(p.Val394Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000355 in 1,612,108 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC16 | NM_020784.3 | c.1180G>C | p.Val394Leu | missense_variant | 13/21 | ENST00000281741.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.1180G>C | p.Val394Leu | missense_variant | 13/21 | 1 | NM_020784.3 | P1 | |
TXNDC16 | ENST00000554399.1 | n.208-42170G>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250272Hom.: 0 AF XY: 0.0000960 AC XY: 13AN XY: 135378
GnomAD4 exome AF: 0.000375 AC: 547AN: 1459974Hom.: 0 Cov.: 30 AF XY: 0.000354 AC XY: 257AN XY: 726342
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.1180G>C (p.V394L) alteration is located in exon 13 (coding exon 11) of the TXNDC16 gene. This alteration results from a G to C substitution at nucleotide position 1180, causing the valine (V) at amino acid position 394 to be replaced by a leucine (L). 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