6-160136229-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_003057.3(SLC22A1):c.849G>A(p.Pro283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,613,426 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
SLC22A1
NM_003057.3 synonymous
NM_003057.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.88
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 6-160136229-G-A is Benign according to our data. Variant chr6-160136229-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 739681.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A1 | NM_003057.3 | c.849G>A | p.Pro283= | synonymous_variant | 5/11 | ENST00000366963.9 | |
SLC22A1 | NM_153187.2 | c.849G>A | p.Pro283= | synonymous_variant | 5/10 | ||
SLC22A1 | XM_005267103.3 | c.849G>A | p.Pro283= | synonymous_variant | 5/12 | ||
SLC22A1 | XM_006715552.3 | c.849G>A | p.Pro283= | synonymous_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A1 | ENST00000366963.9 | c.849G>A | p.Pro283= | synonymous_variant | 5/11 | 1 | NM_003057.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000235 AC: 59AN: 251470Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135914
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GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461244Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 726970
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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Benign
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: -9
Find out detailed SpliceAI scores and Pangolin per-transcript scores at