chr4-67571117-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_012108.4(STAP1):āc.154A>Gā(p.Thr52Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,611,630 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_012108.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAP1 | NM_012108.4 | c.154A>G | p.Thr52Ala | missense_variant | 2/9 | ENST00000265404.7 | |
STAP1 | NM_001317769.2 | c.154A>G | p.Thr52Ala | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAP1 | ENST00000265404.7 | c.154A>G | p.Thr52Ala | missense_variant | 2/9 | 1 | NM_012108.4 | P1 | |
STAP1 | ENST00000396225.1 | c.154A>G | p.Thr52Ala | missense_variant | 2/10 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1459434Hom.: 0 Cov.: 29 AF XY: 0.00000689 AC XY: 5AN XY: 726170
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The p.T52A variant (also known as c.154A>G), located in coding exon 2 of the STAP1 gene, results from an A to G substitution at nucleotide position 154. The threonine at codon 52 is replaced by alanine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at