chr15-45587512-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_012388.4(BLOC1S6):c.69G>A(p.Gly23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000888 in 1,575,894 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G23G) has been classified as Likely benign.
Frequency
Consequence
NM_012388.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLOC1S6 | NM_012388.4 | c.69G>A | p.Gly23= | synonymous_variant | 1/5 | ENST00000220531.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLOC1S6 | ENST00000220531.9 | c.69G>A | p.Gly23= | synonymous_variant | 1/5 | 1 | NM_012388.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000107 AC: 2AN: 186316Hom.: 0 AF XY: 0.0000199 AC XY: 2AN XY: 100432
GnomAD4 exome AF: 0.00000913 AC: 13AN: 1423630Hom.: 0 Cov.: 31 AF XY: 0.0000113 AC XY: 8AN XY: 704950
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74384
ClinVar
Submissions by phenotype
Hermansky-Pudlak syndrome 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at