rs8027174
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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.646+25149G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 455,534 control chromosomes in the GnomAD database, including 1,325 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 0.075 ( 490 hom., cov: 32)
Exomes 𝑓: 0.066 ( 835 hom. )
Consequence
SLCO3A1
NM_013272.4 intron
NM_013272.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.156
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO3A1 | NM_013272.4 | c.646+25149G>T | intron_variant | ENST00000318445.11 | |||
SLCO3A1 | NM_001145044.1 | c.646+25149G>T | intron_variant | ||||
SLCO3A1 | NR_135775.2 | n.573+25149G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO3A1 | ENST00000318445.11 | c.646+25149G>T | intron_variant | 1 | NM_013272.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0748 AC: 11373AN: 152076Hom.: 488 Cov.: 32
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GnomAD3 exomes AF: 0.0550 AC: 7032AN: 127750Hom.: 272 AF XY: 0.0532 AC XY: 3721AN XY: 69958
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GnomAD4 exome AF: 0.0658 AC: 19970AN: 303340Hom.: 835 Cov.: 0 AF XY: 0.0610 AC XY: 10537AN XY: 172780
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GnomAD4 genome ? AF: 0.0749 AC: 11400AN: 152194Hom.: 490 Cov.: 32 AF XY: 0.0727 AC XY: 5412AN XY: 74402
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at