rs1525064
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000306494.11(SLC22A25):c.831-16088A>G variant causes a intron change. The variant allele was found at a frequency of 0.49 in 151,588 control chromosomes in the GnomAD database, including 19,166 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 0.49 ( 19166 hom., cov: 28)
Consequence
SLC22A25
ENST00000306494.11 intron
ENST00000306494.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
No conservation score assigned
Genes affected
SLC22A25 (HGNC:32935): (solute carrier family 22 member 25) Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be integral component of 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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC22A25 | NM_199352.6 | c.831-16088A>G | intron_variant | ENST00000306494.11 | NP_955384.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A25 | ENST00000306494.11 | c.831-16088A>G | intron_variant | 1 | NM_199352.6 | ENSP00000307443 | P1 | |||
SLC22A25 | ENST00000525295.1 | c.403-16088A>G | intron_variant, NMD_transcript_variant | 1 | ENSP00000435614 | |||||
SLC22A25 | ENST00000527057.5 | c.826-16088A>G | intron_variant, NMD_transcript_variant | 1 | ENSP00000432242 | |||||
SLC22A25 | ENST00000528239.5 | c.*480-16088A>G | intron_variant, NMD_transcript_variant | 1 | ENSP00000431235 |
Frequencies
GnomAD3 genomes AF: 0.491 AC: 74309AN: 151470Hom.: 19175 Cov.: 28
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.490 AC: 74315AN: 151588Hom.: 19166 Cov.: 28 AF XY: 0.491 AC XY: 36351AN XY: 74012
GnomAD4 genome
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1586
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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