chr15-92061300-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013272.4(SLCO3A1):c.647-33581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,998 control chromosomes in the GnomAD database, including 27,953 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.60 ( 27953 hom., cov: 32)
Consequence
SLCO3A1
NM_013272.4 intron
NM_013272.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.558
Genes affected
SLCO3A1 (HGNC:10952): (solute carrier organic anion transporter family member 3A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Involved in positive regulation of NF-kappaB transcription factor activity; positive regulation of protein phosphorylation; and prostaglandin transport. Located in plasma membrane. [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=-0.98).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO3A1 | NM_013272.4 | c.647-33581T>C | intron_variant | ENST00000318445.11 | |||
SLCO3A1 | NM_001145044.1 | c.647-33581T>C | intron_variant | ||||
SLCO3A1 | NR_135775.2 | n.574-33581T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO3A1 | ENST00000318445.11 | c.647-33581T>C | intron_variant | 1 | NM_013272.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.597 AC: 90667AN: 151882Hom.: 27930 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.597 AC: 90734AN: 151998Hom.: 27953 Cov.: 32 AF XY: 0.598 AC XY: 44432AN XY: 74282
GnomAD4 genome
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Vascular endothelial growth factor (VEGF) inhibitor response Other:1
association, no assertion criteria provided | case-control | Department of Ophthalmology, College of Medicine, Hanyang University | - | - - |
Computational scores
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Name
Calibrated prediction
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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