rs10493074
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145047.5(OSCP1):c.819+266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 517,406 control chromosomes in the GnomAD database, including 1,599 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 0.072 ( 1232 hom., cov: 33)
Exomes 𝑓: 0.013 ( 367 hom. )
Consequence
OSCP1
NM_145047.5 intron
NM_145047.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.25
Genes affected
OSCP1 (HGNC:29971): (organic solute carrier partner 1) Enables transmembrane transporter activity. Involved in xenobiotic detoxification by transmembrane export across the plasma membrane. Located in basal plasma membrane and cytoplasm. [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=-0.79).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSCP1 | NM_145047.5 | c.819+266C>T | intron_variant | ENST00000235532.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSCP1 | ENST00000235532.9 | c.819+266C>T | intron_variant | 1 | NM_145047.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0722 AC: 10980AN: 152068Hom.: 1226 Cov.: 33
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GnomAD4 exome AF: 0.0129 AC: 4710AN: 365220Hom.: 367 AF XY: 0.0115 AC XY: 2203AN XY: 191972
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GnomAD4 genome ? AF: 0.0724 AC: 11013AN: 152186Hom.: 1232 Cov.: 33 AF XY: 0.0702 AC XY: 5221AN XY: 74416
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ClinVar
Not reported inComputational scores
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Name
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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