rs3828673
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003059.3(SLC22A4):c.652+2104G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,190 control chromosomes in the GnomAD database, including 574 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 0.077 ( 574 hom., cov: 32)
Consequence
SLC22A4
NM_003059.3 intron
NM_003059.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.44
Genes affected
SLC22A4 (HGNC:10968): (solute carrier family 22 member 4) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. The encoded protein is an organic cation transporter and plasma integral membrane protein containing eleven putative transmembrane domains as well as a nucleotide-binding site motif. Transport by this protein is at least partially ATP-dependent. [provided by RefSeq, Jul 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=-0.8).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A4 | NM_003059.3 | c.652+2104G>A | intron_variant | ENST00000200652.4 | |||
MIR3936HG | NR_110997.1 | n.825-3619C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A4 | ENST00000200652.4 | c.652+2104G>A | intron_variant | 1 | NM_003059.3 | P1 | |||
MIR3936HG | ENST00000621103.4 | n.825-3619C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
SLC22A4 | ENST00000491257.1 | n.456+2104G>A | intron_variant, non_coding_transcript_variant | 4 | |||||
MIR3936HG | ENST00000669845.1 | n.451-3619C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0767 AC: 11670AN: 152072Hom.: 577 Cov.: 32
GnomAD3 genomes
?
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11670
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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: 0.0767 AC: 11670AN: 152190Hom.: 574 Cov.: 32 AF XY: 0.0758 AC XY: 5641AN XY: 74394
GnomAD4 genome
?
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11670
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152190
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32
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5641
AN XY:
74394
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429
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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