15-45587494-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_012388.4(BLOC1S6):c.51C>G(p.Pro17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000543 in 1,585,080 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P17P) has been classified as Likely benign.
Frequency
Consequence
NM_012388.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLOC1S6 | NM_012388.4 | c.51C>G | p.Pro17= | synonymous_variant | 1/5 | ENST00000220531.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLOC1S6 | ENST00000220531.9 | c.51C>G | p.Pro17= | synonymous_variant | 1/5 | 1 | NM_012388.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 12AN: 201018Hom.: 1 AF XY: 0.0000645 AC XY: 7AN XY: 108508
GnomAD4 exome AF: 0.0000426 AC: 61AN: 1432826Hom.: 1 Cov.: 30 AF XY: 0.0000408 AC XY: 29AN XY: 710240
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74376
ClinVar
Submissions by phenotype
Hermansky-Pudlak syndrome 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
BLOC1S6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at