chr14-52432428-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020784.3(TXNDC16):c.2354C>T(p.Ser785Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,613,674 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.2354C>T | p.Ser785Leu | missense_variant | 21/21 | ENST00000281741.9 | |
TXNDC16 | NM_001160047.2 | c.2339C>T | p.Ser780Leu | missense_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.2354C>T | p.Ser785Leu | missense_variant | 21/21 | 1 | NM_020784.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152016Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251258Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135822
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461658Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727132
GnomAD4 genome ? AF: 0.0000921 AC: 14AN: 152016Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.2354C>T (p.S785L) alteration is located in exon 21 (coding exon 19) of the TXNDC16 gene. This alteration results from a C to T substitution at nucleotide position 2354, causing the serine (S) at amino acid position 785 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