rs918115
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_058169.6(BORCS5):c.361-2077T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,080 control chromosomes in the GnomAD database, including 5,219 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 0.25 ( 5219 hom., cov: 32)
Consequence
BORCS5
NM_058169.6 intron
NM_058169.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.340
Genes affected
BORCS5 (HGNC:17950): (BLOC-1 related complex subunit 5) Involved in lysosome localization and organelle transport along microtubule. Located in cytoplasmic side of lysosomal membrane and plasma membrane. Is intrinsic component of membrane. Part of BORC complex. Colocalizes with plus-end kinesin complex. [provided by Alliance of Genome Resources, Apr 2022]
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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 = 0.299 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BORCS5 | NM_058169.6 | c.361-2077T>C | intron_variant | ENST00000314565.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BORCS5 | ENST00000314565.9 | c.361-2077T>C | intron_variant | 1 | NM_058169.6 | P1 | |||
BORCS5 | ENST00000298571.6 | c.217-2077T>C | intron_variant | 1 | |||||
BORCS5 | ENST00000542728.5 | c.304-2077T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.250 AC: 38005AN: 151962Hom.: 5219 Cov.: 32
GnomAD3 genomes
?
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38005
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151962
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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: 0.250 AC: 38025AN: 152080Hom.: 5219 Cov.: 32 AF XY: 0.252 AC XY: 18702AN XY: 74338
GnomAD4 genome
?
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AC:
38025
AN:
152080
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32
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18702
AN XY:
74338
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Asia WGS
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380
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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