12-6867538-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM1BP4_StrongBP6BS1BS2
The NM_001159287.1(TPI1):āc.83C>Gā(p.Thr28Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000837 in 1,608,602 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001159287.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPI1 | ENST00000229270.8 | c.83C>G | p.Thr28Ser | missense_variant | Exon 1 of 7 | 1 | ENSP00000229270.4 | |||
TPI1 | ENST00000613953.4 | c.83C>G | p.Thr28Ser | missense_variant | Exon 1 of 7 | 1 | ENSP00000484435.1 | |||
TPI1 | ENST00000396705 | c.-29C>G | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_000365.6 | ENSP00000379933.4 |
Frequencies
GnomAD3 genomes AF: 0.000578 AC: 88AN: 152220Hom.: 2 Cov.: 34
GnomAD3 exomes AF: 0.00159 AC: 377AN: 236626Hom.: 2 AF XY: 0.00197 AC XY: 256AN XY: 129852
GnomAD4 exome AF: 0.000866 AC: 1261AN: 1456270Hom.: 12 Cov.: 34 AF XY: 0.00110 AC XY: 795AN XY: 724190
GnomAD4 genome AF: 0.000558 AC: 85AN: 152332Hom.: 1 Cov.: 34 AF XY: 0.000604 AC XY: 45AN XY: 74488
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | TPI1: BP4, BS2 - |
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Triosephosphate isomerase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 26, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at