chr6-160148750-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_003057.3(SLC22A1):c.1385+5101T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 151,756 control chromosomes in the GnomAD database, including 33 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 0.012 ( 33 hom., cov: 30)
Consequence
SLC22A1
NM_003057.3 intron
NM_003057.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.69
Genes affected
SLC22A1 (HGNC:10963): (solute carrier family 22 member 1) 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. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. Two transcript variants encoding two different isoforms have been found for this gene, but only the longer variant encodes a functional transporter. [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=-0.97).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1851/151756) while in subpopulation AFR AF= 0.0422 (1745/41354). AF 95% confidence interval is 0.0405. There are 33 homozygotes in gnomad4. There are 882 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 33 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC22A1 | NM_003057.3 | c.1385+5101T>G | intron_variant | ENST00000366963.9 | NP_003048.1 | |||
SLC22A1 | NM_153187.2 | c.1385+5101T>G | intron_variant | NP_694857.1 | ||||
SLC22A1 | XM_005267103.3 | c.1385+5101T>G | intron_variant | XP_005267160.1 | ||||
SLC22A1 | XM_006715552.3 | c.1385+5101T>G | intron_variant | XP_006715615.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A1 | ENST00000366963.9 | c.1385+5101T>G | intron_variant | 1 | NM_003057.3 | ENSP00000355930 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0122 AC: 1849AN: 151640Hom.: 33 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0122 AC: 1851AN: 151756Hom.: 33 Cov.: 30 AF XY: 0.0119 AC XY: 882AN XY: 74156
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ClinVar
Not reported inComputational scores
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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