1-9356564-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025106.4(SPSB1):c.673C>T(p.Arg225Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000763 in 1,598,680 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025106.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPSB1 | NM_025106.4 | c.673C>T | p.Arg225Cys | missense_variant | Exon 2 of 3 | ENST00000328089.11 | NP_079382.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPSB1 | ENST00000328089.11 | c.673C>T | p.Arg225Cys | missense_variant | Exon 2 of 3 | 1 | NM_025106.4 | ENSP00000330221.6 | ||
SPSB1 | ENST00000377399.2 | c.673C>T | p.Arg225Cys | missense_variant | Exon 1 of 2 | 1 | ENSP00000366616.2 | |||
SPSB1 | ENST00000357898.3 | c.673C>T | p.Arg225Cys | missense_variant | Exon 2 of 3 | 5 | ENSP00000350573.3 | |||
SPSB1 | ENST00000450402.1 | c.*67C>T | downstream_gene_variant | 5 | ENSP00000409235.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000248 AC: 6AN: 241792Hom.: 0 AF XY: 0.0000306 AC XY: 4AN XY: 130810
GnomAD4 exome AF: 0.0000795 AC: 115AN: 1446496Hom.: 0 Cov.: 33 AF XY: 0.0000851 AC XY: 61AN XY: 716522
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.673C>T (p.R225C) alteration is located in exon 2 (coding exon 1) of the SPSB1 gene. This alteration results from a C to T substitution at nucleotide position 673, causing the arginine (R) at amino acid position 225 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