rs273915
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003059.3(SLC22A4):c.824+2071G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 151,722 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000020 ( 0 hom., cov: 28)
Consequence
SLC22A4
NM_003059.3 intron
NM_003059.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.265
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A4 | NM_003059.3 | c.824+2071G>A | intron_variant | ENST00000200652.4 | |||
MIR3936HG | NR_110997.1 | n.824+7763C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A4 | ENST00000200652.4 | c.824+2071G>A | intron_variant | 1 | NM_003059.3 | P1 | |||
MIR3936HG | ENST00000621103.4 | n.824+7763C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
SLC22A4 | ENST00000425923.1 | n.173-35G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
MIR3936HG | ENST00000669845.1 | n.450+7763C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151722Hom.: 0 Cov.: 28
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GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151722Hom.: 0 Cov.: 28 AF XY: 0.0000270 AC XY: 2AN XY: 74076
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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