chr6-160132240-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003057.3(SLC22A1):c.524G>T(p.Arg175Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000701 in 1,426,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R175C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003057.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A1 | NM_003057.3 | c.524G>T | p.Arg175Leu | missense_variant | 3/11 | ENST00000366963.9 | |
SLC22A1 | NM_153187.2 | c.524G>T | p.Arg175Leu | missense_variant | 3/10 | ||
SLC22A1 | XM_005267103.3 | c.524G>T | p.Arg175Leu | missense_variant | 3/12 | ||
SLC22A1 | XM_006715552.3 | c.524G>T | p.Arg175Leu | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A1 | ENST00000366963.9 | c.524G>T | p.Arg175Leu | missense_variant | 3/11 | 1 | NM_003057.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000441 AC: 1AN: 226988Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122498
GnomAD4 exome AF: 7.01e-7 AC: 1AN: 1426458Hom.: 0 Cov.: 31 AF XY: 0.00000142 AC XY: 1AN XY: 706712
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | The c.524G>T (p.R175L) alteration is located in exon 3 (coding exon 3) of the SLC22A1 gene. This alteration results from a G to T substitution at nucleotide position 524, causing the arginine (R) at amino acid position 175 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at