rs1055060
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032641.4(SPSB2):c.*252T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 674,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00035 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000044 ( 0 hom. )
Consequence
SPSB2
NM_032641.4 3_prime_UTR
NM_032641.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.789
Genes affected
TPI1 (HGNC:12009): (triosephosphate isomerase 1) This gene encodes an enzyme, consisting of two identical proteins, which catalyzes the isomerization of glyceraldehydes 3-phosphate (G3P) and dihydroxy-acetone phosphate (DHAP) in glycolysis and gluconeogenesis. Mutations in this gene are associated with triosephosphate isomerase deficiency. Pseudogenes have been identified on chromosomes 1, 4, 6 and 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
SPSB2 (HGNC:29522): (splA/ryanodine receptor domain and SOCS box containing 2) This gene encodes a member of a subfamily of proteins containing a central SPRY (repeats in splA and RyR) domain and a C-terminal suppressor of cytokine signaling (SOCS) box. This protein plays a role in cell signaling. This gene is present in a gene-rich cluster on chromosome 12p13 in the vicinity of the CD4 antigen and triosephosphate isomerase genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPI1 | NM_000365.6 | c.*557A>G | 3_prime_UTR_variant | 7/7 | ENST00000396705.10 | ||
SPSB2 | NM_032641.4 | c.*252T>C | 3_prime_UTR_variant | 3/3 | ENST00000524270.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPI1 | ENST00000396705.10 | c.*557A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_000365.6 | P1 | ||
SPSB2 | ENST00000524270.6 | c.*252T>C | 3_prime_UTR_variant | 3/3 | 1 | NM_032641.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000349 AC: 53AN: 151776Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000322 AC: 4AN: 124232Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67952
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GnomAD4 exome AF: 0.0000440 AC: 23AN: 522992Hom.: 0 Cov.: 4 AF XY: 0.0000282 AC XY: 8AN XY: 284058
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GnomAD4 genome ? AF: 0.000349 AC: 53AN: 151866Hom.: 0 Cov.: 33 AF XY: 0.000337 AC XY: 25AN XY: 74218
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at