5-134887922-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024715.4(TXNDC15):c.331G>A(p.Gly111Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,614,034 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_024715.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TXNDC15 | NM_024715.4 | c.331G>A | p.Gly111Ser | missense_variant | 2/5 | ENST00000358387.9 | NP_078991.3 | |
TXNDC15 | NM_001350735.2 | c.127G>A | p.Gly43Ser | missense_variant | 2/5 | NP_001337664.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TXNDC15 | ENST00000358387.9 | c.331G>A | p.Gly111Ser | missense_variant | 2/5 | 1 | NM_024715.4 | ENSP00000351157 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251420Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135892
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461832Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727218
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74344
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.331G>A (p.G111S) alteration is located in exon 2 (coding exon 2) of the TXNDC15 gene. This alteration results from a G to A substitution at nucleotide position 331, causing the glycine (G) at amino acid position 111 to be replaced by a serine (S). 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