chr16-28320469-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001024401.3(SBK1):c.823C>A(p.Pro275Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000211 in 1,422,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001024401.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SBK1 | ENST00000341901.5 | c.823C>A | p.Pro275Thr | missense_variant | Exon 4 of 4 | 1 | NM_001024401.3 | ENSP00000343248.4 | ||
SBK1 | ENST00000671413.3 | c.1087C>A | p.Pro363Thr | missense_variant | Exon 4 of 4 | ENSP00000499661.3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000485 AC: 1AN: 206186Hom.: 0 AF XY: 0.00000862 AC XY: 1AN XY: 116022
GnomAD4 exome AF: 0.00000211 AC: 3AN: 1422412Hom.: 0 Cov.: 32 AF XY: 0.00000283 AC XY: 2AN XY: 707806
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.823C>A (p.P275T) alteration is located in exon 4 (coding exon 3) of the SBK1 gene. This alteration results from a C to A substitution at nucleotide position 823, causing the proline (P) at amino acid position 275 to be replaced by a threonine (T). 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