chr4-67558927-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012108.4(STAP1):c.118C>T(p.Arg40Trp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,610,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R40Q) has been classified as Likely benign.
Frequency
Consequence
NM_012108.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
STAP1 | NM_012108.4 | c.118C>T | p.Arg40Trp | missense_variant, splice_region_variant | 1/9 | ENST00000265404.7 | |
STAP1 | NM_001317769.2 | c.118C>T | p.Arg40Trp | missense_variant, splice_region_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAP1 | ENST00000265404.7 | c.118C>T | p.Arg40Trp | missense_variant, splice_region_variant | 1/9 | 1 | NM_012108.4 | P1 | |
STAP1 | ENST00000396225.1 | c.118C>T | p.Arg40Trp | missense_variant, splice_region_variant | 1/10 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151906Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248270Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134328
GnomAD4 exome AF: 0.0000343 AC: 50AN: 1458282Hom.: 0 Cov.: 30 AF XY: 0.0000262 AC XY: 19AN XY: 725518
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151906Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74158
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 04, 2022 | The p.R40W variant (also known as c.118C>T), located in coding exon 1 of the STAP1 gene, results from a C to T substitution at nucleotide position 118. The arginine at codon 40 is replaced by tryptophan, an amino acid with dissimilar 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