rs9302356
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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.*1544T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 984,790 control chromosomes in the GnomAD database, including 197,796 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 0.62 ( 29628 hom., cov: 32)
Exomes 𝑓: 0.63 ( 168168 hom. )
Consequence
SLCO3A1
NM_013272.4 3_prime_UTR
NM_013272.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.330
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=-0.83).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO3A1 | NM_013272.4 | c.*1544T>C | 3_prime_UTR_variant | 10/10 | ENST00000318445.11 | ||
SLCO3A1 | NM_001145044.1 | c.1996+1681T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO3A1 | ENST00000318445.11 | c.*1544T>C | 3_prime_UTR_variant | 10/10 | 1 | NM_013272.4 | P1 | ||
ENST00000557683.1 | n.418-1760A>G | intron_variant, non_coding_transcript_variant | 4 | ||||||
ENST00000561674.1 | n.186-7438A>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.619 AC: 93978AN: 151830Hom.: 29609 Cov.: 32
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GnomAD4 exome AF: 0.634 AC: 528211AN: 832842Hom.: 168168 Cov.: 35 AF XY: 0.635 AC XY: 244175AN XY: 384604
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GnomAD4 genome ? AF: 0.619 AC: 94036AN: 151948Hom.: 29628 Cov.: 32 AF XY: 0.612 AC XY: 45434AN XY: 74272
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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