5-134887974-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_024715.4(TXNDC15):c.383A>G(p.Glu128Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,614,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024715.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC15 | NM_024715.4 | c.383A>G | p.Glu128Gly | missense_variant | 2/5 | ENST00000358387.9 | |
TXNDC15 | NM_001350735.2 | c.179A>G | p.Glu60Gly | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC15 | ENST00000358387.9 | c.383A>G | p.Glu128Gly | missense_variant | 2/5 | 1 | NM_024715.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000290 AC: 73AN: 251438Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135894
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 727242
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at