NM_004334.3:c.260C>A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004334.3(BST1):c.260C>A(p.Pro87His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,802 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P87L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BST1 | ENST00000265016.9 | c.260C>A | p.Pro87His | missense_variant | Exon 2 of 9 | 1 | NM_004334.3 | ENSP00000265016.4 | ||
BST1 | ENST00000382346.7 | c.305C>A | p.Pro102His | missense_variant | Exon 3 of 10 | 5 | ENSP00000371783.3 | |||
ENSG00000288606 | ENST00000504598.5 | n.*21C>A | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251230Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135786
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461638Hom.: 0 Cov.: 30 AF XY: 0.0000371 AC XY: 27AN XY: 727152
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.260C>A (p.P87H) alteration is located in exon 2 (coding exon 2) of the BST1 gene. This alteration results from a C to A substitution at nucleotide position 260, causing the proline (P) at amino acid position 87 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