12-20815710-AATATTCACTTGGTATCTG-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_019844.4(SLCO1B3):c.-28_-11delATATTCACTTGGTATCTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,469,848 control chromosomes in the GnomAD database, including 54,843 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.23 ( 4628 hom., cov: 23)
Exomes 𝑓: 0.27 ( 50215 hom. )
Consequence
SLCO1B3
NM_019844.4 5_prime_UTR
NM_019844.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.607
Genes affected
SLCO1B3 (HGNC:10961): (solute carrier organic anion transporter family member 1B3) This gene encodes a liver-specific member of the organic anion transporter family. The encoded protein is a transmembrane receptor that mediates the sodium-independent uptake of endogenous and xenobiotic compounds and plays a critical role in bile acid and bilirubin transport. Mutations in this gene are a cause of Rotor type hyperbilirubinemia. Alternative splicing of this gene and the use of alternative promoters results in transcript variants encoding different isoforms that differ in their tissue specificity. [provided by RefSeq, Mar 2017]
SLCO1B3-SLCO1B7 (HGNC:54403): (SLCO1B3-SLCO1B7 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring SLCO1B3 (solute carrier organic anion transporter family member 1B3) and SLCO1B7 (solute carrier organic anion transporter family member 1B7 (putative)) genes on chromosome 12. The readthrough transcript encodes a protein that shares sequence identity with both the upstream and downstream genes. [provided by RefSeq, Jun 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 12-20815710-AATATTCACTTGGTATCTG-A is Benign according to our data. Variant chr12-20815710-AATATTCACTTGGTATCTG-A is described in ClinVar as [Benign]. Clinvar id is 993345.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1B3 | NM_019844.4 | c.-28_-11delATATTCACTTGGTATCTG | 5_prime_UTR_variant | 3/16 | ENST00000381545.8 | NP_062818.1 | ||
SLCO1B3-SLCO1B7 | NM_001371097.1 | c.-28_-11delATATTCACTTGGTATCTG | 5_prime_UTR_variant | 1/16 | NP_001358026.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1B3 | ENST00000381545.8 | c.-28_-11delATATTCACTTGGTATCTG | 5_prime_UTR_variant | 3/16 | 2 | NM_019844.4 | ENSP00000370956.4 | |||
SLCO1B3-SLCO1B7 | ENST00000540229.1 | c.-28_-11delATATTCACTTGGTATCTG | 5_prime_UTR_variant | 1/16 | 2 | ENSP00000441269.1 |
Frequencies
GnomAD3 genomes AF: 0.234 AC: 35565AN: 152042Hom.: 4629 Cov.: 23
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GnomAD3 exomes AF: 0.140 AC: 29724AN: 212094Hom.: 3670 AF XY: 0.149 AC XY: 17141AN XY: 115188
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GnomAD4 exome AF: 0.272 AC: 358538AN: 1317686Hom.: 50215 AF XY: 0.269 AC XY: 177123AN XY: 659148
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GnomAD4 genome AF: 0.234 AC: 35591AN: 152162Hom.: 4628 Cov.: 23 AF XY: 0.230 AC XY: 17135AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Rotor syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 30, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at