17-58308839-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004758.4(TSPOAP1):c.4433G>A(p.Arg1478His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,611,210 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 Uncertain significance (★).
Frequency
Consequence
NM_004758.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPOAP1 | NM_004758.4 | c.4433G>A | p.Arg1478His | missense_variant | 22/32 | ENST00000343736.9 | NP_004749.2 | |
TSPOAP1 | NM_001261835.2 | c.4433G>A | p.Arg1478His | missense_variant | 22/32 | NP_001248764.1 | ||
TSPOAP1 | NM_024418.3 | c.4253G>A | p.Arg1418His | missense_variant | 21/31 | NP_077729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPOAP1 | ENST00000343736.9 | c.4433G>A | p.Arg1478His | missense_variant | 22/32 | 1 | NM_004758.4 | ENSP00000345824 | P2 | |
TSPOAP1 | ENST00000268893.10 | c.4253G>A | p.Arg1418His | missense_variant | 21/31 | 1 | ENSP00000268893 | A2 | ||
TSPOAP1 | ENST00000580669.6 | c.1829G>A | p.Arg610His | missense_variant | 6/16 | 5 | ENSP00000462822 | |||
TSPOAP1 | ENST00000582679.1 | c.422-898G>A | intron_variant | 5 | ENSP00000462710 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000331 AC: 8AN: 241518Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132568
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1458982Hom.: 0 Cov.: 42 AF XY: 0.0000152 AC XY: 11AN XY: 725642
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.4433G>A (p.R1478H) alteration is located in exon 22 (coding exon 22) of the TSPOAP1 gene. This alteration results from a G to A substitution at nucleotide position 4433, causing the arginine (R) at amino acid position 1478 to be replaced by a histidine (H). 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