6-3273069-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015482.2(SLC22A23):c.2047A>T(p.Met683Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000766 in 1,566,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015482.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC22A23 | NM_015482.2 | c.2047A>T | p.Met683Leu | missense_variant | 10/10 | ENST00000406686.8 | NP_056297.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A23 | ENST00000406686.8 | c.2047A>T | p.Met683Leu | missense_variant | 10/10 | 5 | NM_015482.2 | ENSP00000385028 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000452 AC: 1AN: 221262Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 119920
GnomAD4 exome AF: 0.00000778 AC: 11AN: 1414730Hom.: 0 Cov.: 30 AF XY: 0.00000858 AC XY: 6AN XY: 699094
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.2047A>T (p.M683L) alteration is located in exon 10 (coding exon 10) of the SLC22A23 gene. This alteration results from a A to T substitution at nucleotide position 2047, causing the methionine (M) at amino acid position 683 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