chr14-52482847-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020784.3(TXNDC16):c.1227C>G(p.Asp409Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,611,786 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.1227C>G | p.Asp409Glu | missense_variant | 13/21 | ENST00000281741.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.1227C>G | p.Asp409Glu | missense_variant | 13/21 | 1 | NM_020784.3 | P1 | |
TXNDC16 | ENST00000554399.1 | n.208-42123C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249804Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135132
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459528Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726162
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.1227C>G (p.D409E) alteration is located in exon 13 (coding exon 11) of the TXNDC16 gene. This alteration results from a C to G substitution at nucleotide position 1227, causing the aspartic acid (D) at amino acid position 409 to be replaced by a glutamic acid (E). 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