rs3811976
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_180991.5(SLCO4C1):c.*2326A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,546 control chromosomes in the GnomAD database, including 637 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 0.088 ( 635 hom., cov: 33)
Exomes 𝑓: 0.092 ( 2 hom. )
Consequence
SLCO4C1
NM_180991.5 3_prime_UTR
NM_180991.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.77
Genes affected
SLCO4C1 (HGNC:23612): (solute carrier organic anion transporter family member 4C1) SLCO4C1 belongs to the organic anion transporter (OATP) family. OATPs are involved in the membrane transport of bile acids, conjugated steroids, thyroid hormone, eicosanoids, peptides, and numerous drugs in many tissues (Mikkaichi et al., 2004 [PubMed 14993604]).[supplied by OMIM, Mar 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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO4C1 | NM_180991.5 | c.*2326A>G | 3_prime_UTR_variant | 13/13 | ENST00000310954.7 | ||
SLCO4C1 | XM_011543370.3 | c.*2326A>G | 3_prime_UTR_variant | 12/12 | |||
SLCO4C1 | XM_011543372.2 | c.*2326A>G | 3_prime_UTR_variant | 15/15 | |||
SLCO4C1 | XM_047417146.1 | c.*2326A>G | 3_prime_UTR_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO4C1 | ENST00000310954.7 | c.*2326A>G | 3_prime_UTR_variant | 13/13 | 1 | NM_180991.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0883 AC: 13427AN: 152134Hom.: 635 Cov.: 33
GnomAD3 genomes
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33
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GnomAD4 exome AF: 0.0918 AC: 27AN: 294Hom.: 2 Cov.: 0 AF XY: 0.0928 AC XY: 18AN XY: 194
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GnomAD4 genome ? AF: 0.0882 AC: 13432AN: 152252Hom.: 635 Cov.: 33 AF XY: 0.0897 AC XY: 6675AN XY: 74440
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ClinVar
Not reported inComputational scores
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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