11-64562342-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018484.4(SLC22A11):c.728C>T(p.Ala243Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000583 in 1,610,970 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A11 | NM_018484.4 | c.728C>T | p.Ala243Val | missense_variant | 4/10 | ENST00000301891.9 | |
SLC22A11 | NM_001307985.2 | c.728C>T | p.Ala243Val | missense_variant | 4/8 | ||
SLC22A11 | XM_011545167.2 | c.329C>T | p.Ala110Val | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A11 | ENST00000301891.9 | c.728C>T | p.Ala243Val | missense_variant | 4/10 | 1 | NM_018484.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152182Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000100 AC: 25AN: 248912Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134926
GnomAD4 exome AF: 0.0000596 AC: 87AN: 1458788Hom.: 0 Cov.: 31 AF XY: 0.0000565 AC XY: 41AN XY: 725284
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152182Hom.: 1 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.728C>T (p.A243V) alteration is located in exon 4 (coding exon 4) of the SLC22A11 gene. This alteration results from a C to T substitution at nucleotide position 728, causing the alanine (A) at amino acid position 243 to be replaced by a valine (V). 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