chr11-64562023-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018484.4(SLC22A11):c.517C>A(p.Leu173Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,248 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018484.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC22A11 | NM_018484.4 | c.517C>A | p.Leu173Met | missense_variant | Exon 3 of 10 | ENST00000301891.9 | NP_060954.1 | |
SLC22A11 | NM_001307985.2 | c.517C>A | p.Leu173Met | missense_variant | Exon 3 of 8 | NP_001294914.1 | ||
SLC22A11 | XM_011545167.2 | c.118C>A | p.Leu40Met | missense_variant | Exon 2 of 9 | XP_011543469.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250102Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135420
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461044Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726798
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.517C>A (p.L173M) alteration is located in exon 3 (coding exon 3) of the SLC22A11 gene. This alteration results from a C to A substitution at nucleotide position 517, causing the leucine (L) at amino acid position 173 to be replaced by a methionine (M). 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