rs11231379
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001136506.2(SLC22A24):c.403-2695G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,160 control chromosomes in the GnomAD database, including 1,240 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 0.12 ( 1240 hom., cov: 32)
Consequence
SLC22A24
NM_001136506.2 intron
NM_001136506.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.124
Genes affected
SLC22A24 (HGNC:28542): (solute carrier family 22 member 24) SLC22A24 belongs to a large family of transmembrane proteins that function as uniporters, symporters, and antiporters to transport organic ions across cell membranes (Jacobsson et al., 2007 [PubMed 17714910]).[supplied by OMIM, Mar 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=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A24 | NM_001136506.2 | c.403-2695G>C | intron_variant | ENST00000612278.4 | |||
SLC22A24 | NM_173586.3 | c.403-2695G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A24 | ENST00000612278.4 | c.403-2695G>C | intron_variant | 5 | NM_001136506.2 | P4 | |||
SLC22A24 | ENST00000326192.5 | c.403-2695G>C | intron_variant | 1 | |||||
SLC22A24 | ENST00000417740.5 | c.403-2695G>C | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.120 AC: 18288AN: 152042Hom.: 1237 Cov.: 32
GnomAD3 genomes
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18288
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152042
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.120 AC: 18304AN: 152160Hom.: 1240 Cov.: 32 AF XY: 0.121 AC XY: 9016AN XY: 74386
GnomAD4 genome
?
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AC:
18304
AN:
152160
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32
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9016
AN XY:
74386
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452
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3478
ClinVar
Not reported inComputational scores
Source:
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