12-55716125-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001487.4(BLOC1S1):c.74C>T(p.Pro25Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,610,258 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_001487.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
BLOC1S1 | ENST00000548925.6 | c.74C>T | p.Pro25Leu | missense_variant | Exon 1 of 4 | 1 | NM_001487.4 | ENSP00000447537.1 | ||
ENSG00000258311 | ENST00000550412.5 | c.74C>T | p.Pro25Leu | missense_variant | Exon 1 of 4 | 2 | ENSP00000447650.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000207 AC: 5AN: 241852Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131118
GnomAD4 exome AF: 0.0000384 AC: 56AN: 1458064Hom.: 0 Cov.: 30 AF XY: 0.0000359 AC XY: 26AN XY: 725078
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.74C>T (p.P25L) alteration is located in exon 1 (coding exon 1) of the BLOC1S1 gene. This alteration results from a C to T substitution at nucleotide position 74, causing the proline (P) at amino acid position 25 to be replaced by a leucine (L). 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