rs2893808
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_194298.3(SLC16A9):c.*838G>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 0.0297 in 152,216 control chromosomes in the GnomAD database, including 103 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 0.030 ( 103 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC16A9
NM_194298.3 3_prime_UTR
NM_194298.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.38
Genes affected
SLC16A9 (HGNC:23520): (solute carrier family 16 member 9) Predicted to enable monocarboxylic acid transmembrane transporter activity. Involved in urate metabolic process. Predicted to be integral component of 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=-0.66).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0297 (4520/152216) while in subpopulation NFE AF= 0.0451 (3066/68014). AF 95% confidence interval is 0.0437. There are 103 homozygotes in gnomad4. There are 2171 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 103 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC16A9 | NM_194298.3 | c.*838G>A | 3_prime_UTR_variant | 6/6 | ENST00000395348.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC16A9 | ENST00000395348.8 | c.*838G>A | 3_prime_UTR_variant | 6/6 | 5 | NM_194298.3 | P1 | ||
SLC16A9 | ENST00000395347.1 | c.*838G>A | 3_prime_UTR_variant | 6/6 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0297 AC: 4520AN: 152098Hom.: 103 Cov.: 33
GnomAD3 genomes
?
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33
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.0297 AC: 4520AN: 152216Hom.: 103 Cov.: 33 AF XY: 0.0292 AC XY: 2171AN XY: 74418
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?
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33
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31
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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