6-8054272-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001199322.1(BLOC1S5):āc.1A>Gā(p.Met1?) variant causes a start lost, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 452,292 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001199322.1 start_lost, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BLOC1S5 | NM_201280.3 | c.195+8262A>G | intron_variant | ENST00000397457.7 | NP_958437.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BLOC1S5 | ENST00000397457.7 | c.195+8262A>G | intron_variant | 1 | NM_201280.3 | ENSP00000380598.2 | ||||
EEF1E1-BLOC1S5 | ENST00000397456.2 | n.*11+8262A>G | intron_variant | 3 | ENSP00000380597.2 | |||||
BLOC1S5-TXNDC5 | ENST00000439343.2 | n.183+8262A>G | intron_variant | 2 | ENSP00000454697.1 |
Frequencies
GnomAD3 genomes AF: 0.00747 AC: 1137AN: 152152Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00140 AC: 183AN: 130398Hom.: 1 AF XY: 0.00115 AC XY: 82AN XY: 71346
GnomAD4 exome AF: 0.000873 AC: 262AN: 300022Hom.: 3 Cov.: 0 AF XY: 0.000689 AC XY: 118AN XY: 171280
GnomAD4 genome AF: 0.00755 AC: 1149AN: 152270Hom.: 11 Cov.: 33 AF XY: 0.00733 AC XY: 546AN XY: 74454
ClinVar
Submissions by phenotype
BLOC1S5-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 26, 2021 | 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