rs4285028
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021082.4(SLC15A2):c.*810A>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 0.222 in 152,152 control chromosomes in the GnomAD database, including 4,546 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 0.22 ( 4546 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
SLC15A2
NM_021082.4 3_prime_UTR
NM_021082.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.393
Genes affected
SLC15A2 (HGNC:10921): (solute carrier family 15 member 2) The mammalian kidney expresses a proton-coupled peptide transporter that is responsible for the absorption of small peptides, as well as beta-lactam antibiotics and other peptide-like drugs, from the tubular filtrate. This transporter, SLC15A2, belongs to the same gene family as SLC15A1 (MIM 600544), the proton-coupled peptide transporter found in the small intestine (Liu et al, 1995 [PubMed 7756356]).[supplied by OMIM, Feb 2011]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC15A2 | NM_021082.4 | c.*810A>C | 3_prime_UTR_variant | 22/22 | ENST00000489711.6 | ||
SLC15A2 | NM_001145998.2 | c.*810A>C | 3_prime_UTR_variant | 21/21 | |||
SLC15A2 | XM_005247722.4 | c.*810A>C | 3_prime_UTR_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC15A2 | ENST00000489711.6 | c.*810A>C | 3_prime_UTR_variant | 22/22 | 1 | NM_021082.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.222 AC: 33800AN: 152032Hom.: 4541 Cov.: 32
GnomAD3 genomes
?
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32
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GnomAD4 exome AF: 0.500 AC: 1AN: 2Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome ? AF: 0.222 AC: 33813AN: 152150Hom.: 4546 Cov.: 32 AF XY: 0.224 AC XY: 16676AN XY: 74358
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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