rs3088442
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021977.4(SLC22A3):c.*564G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 157,666 control chromosomes in the GnomAD database, including 8,171 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 0.29 ( 7757 hom., cov: 32)
Exomes 𝑓: 0.37 ( 414 hom. )
Consequence
SLC22A3
NM_021977.4 3_prime_UTR
NM_021977.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.47
Genes affected
SLC22A3 (HGNC:10967): (solute carrier family 22 member 3) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. [provided by RefSeq, Jul 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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A3 | NM_021977.4 | c.*564G>A | 3_prime_UTR_variant | 11/11 | ENST00000275300.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A3 | ENST00000275300.3 | c.*564G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_021977.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.288 AC: 43726AN: 151978Hom.: 7743 Cov.: 32
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GnomAD4 exome AF: 0.369 AC: 2056AN: 5570Hom.: 414 Cov.: 0 AF XY: 0.369 AC XY: 1066AN XY: 2890
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GnomAD4 genome ? AF: 0.288 AC: 43754AN: 152096Hom.: 7757 Cov.: 32 AF XY: 0.286 AC XY: 21230AN XY: 74338
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at