rs476037
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_144585.4(SLC22A12):c.*517G>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 0.12 in 203,516 control chromosomes in the GnomAD database, including 1,950 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.12 ( 1424 hom., cov: 32)
Exomes 𝑓: 0.12 ( 526 hom. )
Consequence
SLC22A12
NM_144585.4 3_prime_UTR
NM_144585.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0230
Genes affected
SLC22A12 (HGNC:17989): (solute carrier family 22 member 12) The protein encoded by this gene is a member of the organic anion transporter (OAT) family, and it acts as a urate transporter to regulate urate levels in blood. This protein is an integral membrane protein primarily found in epithelial cells of the proximal tubule of the kidney. An elevated level of serum urate, hyperuricemia, is associated with increased incidences of gout, and mutations in this gene cause renal hypouricemia type 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BP6
?
Variant 11-64602068-G-A is Benign according to our data. Variant chr11-64602068-G-A is described in ClinVar as [Benign]. Clinvar id is 305257.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A12 | NM_144585.4 | c.*517G>A | 3_prime_UTR_variant | 10/10 | ENST00000377574.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A12 | ENST00000377574.6 | c.*517G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_144585.4 | P1 | ||
SLC22A12 | ENST00000377572.5 | c.*517G>A | 3_prime_UTR_variant | 8/8 | 1 | ||||
SLC22A12 | ENST00000377567.6 | c.*517G>A | 3_prime_UTR_variant | 9/9 | 5 | ||||
SLC22A12 | ENST00000473690.5 | c.*517G>A | 3_prime_UTR_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18114AN: 151820Hom.: 1424 Cov.: 32
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GnomAD4 exome AF: 0.123 AC: 6342AN: 51578Hom.: 526 Cov.: 0 AF XY: 0.129 AC XY: 3528AN XY: 27268
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GnomAD4 genome ? AF: 0.119 AC: 18131AN: 151938Hom.: 1424 Cov.: 32 AF XY: 0.127 AC XY: 9403AN XY: 74252
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Dalmatian hypouricemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational 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