rs2294436
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_201280.3(BLOC1S5):c.195+5079T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,206 control chromosomes in the GnomAD database, including 1,936 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 1936 hom., cov: 32)
Consequence
BLOC1S5
NM_201280.3 intron
NM_201280.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.840
Genes affected
BLOC1S5 (HGNC:18561): (biogenesis of lysosomal organelles complex 1 subunit 5) This gene encodes a component of BLOC-1 (biogenesis of lysosome-related organelles complex 1). Components of this complex are involved in the biogenesis of organelles such as melanosomes and platelet-dense granules. A mouse model for Hermansky-Pudlak Syndrome is mutated in the murine version of this gene. Alternative splicing results in multiple transcript variants. Read-through transcription exists between this gene and the upstream EEF1E1 (eukaryotic translation elongation factor 1 epsilon 1) gene, as well as with the downstream TXNDC5 (thioredoxin domain containing 5) gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLOC1S5 | NM_201280.3 | c.195+5079T>C | intron_variant | ENST00000397457.7 | |||
BLOC1S5-TXNDC5 | NR_037616.1 | n.233+5079T>C | intron_variant, non_coding_transcript_variant | ||||
EEF1E1-BLOC1S5 | NR_037618.1 | n.541+5079T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLOC1S5 | ENST00000397457.7 | c.195+5079T>C | intron_variant | 1 | NM_201280.3 | P1 | |||
BLOC1S5 | ENST00000244777.6 | c.195+5079T>C | intron_variant, NMD_transcript_variant | 1 | |||||
BLOC1S5 | ENST00000627748.2 | c.196-3083T>C | intron_variant, NMD_transcript_variant | 1 | |||||
BLOC1S5 | ENST00000543936.7 | c.195+5079T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.156 AC: 23769AN: 152088Hom.: 1933 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.156 AC: 23785AN: 152206Hom.: 1936 Cov.: 32 AF XY: 0.155 AC XY: 11557AN XY: 74418
GnomAD4 genome
?
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23785
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32
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11557
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74418
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391
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at