17-58308621-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004758.4(TSPOAP1):c.4651C>T(p.Arg1551Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,448,926 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
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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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPOAP1 | NM_004758.4 | c.4651C>T | p.Arg1551Cys | missense_variant | 22/32 | ENST00000343736.9 | NP_004749.2 | |
TSPOAP1 | NM_001261835.2 | c.4651C>T | p.Arg1551Cys | missense_variant | 22/32 | NP_001248764.1 | ||
TSPOAP1 | NM_024418.3 | c.4471C>T | p.Arg1491Cys | missense_variant | 21/31 | NP_077729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPOAP1 | ENST00000343736.9 | c.4651C>T | p.Arg1551Cys | missense_variant | 22/32 | 1 | NM_004758.4 | ENSP00000345824 | P2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000812 AC: 2AN: 246394Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133622
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1448926Hom.: 0 Cov.: 31 AF XY: 0.0000139 AC XY: 10AN XY: 718752
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.4651C>T (p.R1551C) alteration is located in exon 22 (coding exon 22) of the TSPOAP1 gene. This alteration results from a C to T substitution at nucleotide position 4651, causing the arginine (R) at amino acid position 1551 to be replaced by a cysteine (C). 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