rs2306231
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000307378.10(SLCO1A2):c.-62-2738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,742 control chromosomes in the GnomAD database, including 11,288 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 0.37 ( 11288 hom., cov: 32)
Consequence
SLCO1A2
ENST00000307378.10 intron
ENST00000307378.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.124
Genes affected
SLCO1A2 (HGNC:10956): (solute carrier organic anion transporter family member 1A2) This gene encodes a sodium-independent transporter which mediates cellular uptake of organic ions in the liver. Its substrates include bile acids, bromosulphophthalein, and some steroidal compounds. The protein is a member of the SLC21A family of solute carriers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2008]
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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=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1A2 | NM_001386878.1 | c.-62-2738T>C | intron_variant | ||||
SLCO1A2 | NM_001386881.1 | c.-57-2743T>C | intron_variant | ||||
SLCO1A2 | NM_001386882.2 | c.-62-2738T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1A2 | ENST00000307378.10 | c.-62-2738T>C | intron_variant | 1 | P1 | ||||
SLCO1A2 | ENST00000413682.5 | c.-311-2743T>C | intron_variant | 4 | |||||
SLCO1A2 | ENST00000416627.1 | c.-62-2738T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.373 AC: 56499AN: 151624Hom.: 11263 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: 0.373 AC: 56566AN: 151742Hom.: 11288 Cov.: 32 AF XY: 0.370 AC XY: 27473AN XY: 74164
GnomAD4 genome
?
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56566
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32
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27473
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74164
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1158
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3474
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