chr20-4857181-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005116.6(SLC23A2):c.1744C>T(p.Arg582Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,607,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005116.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC23A2 | NM_005116.6 | c.1744C>T | p.Arg582Trp | missense_variant | 17/17 | ENST00000338244.6 | |
SLC23A2 | NM_203327.2 | c.1744C>T | p.Arg582Trp | missense_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC23A2 | ENST00000338244.6 | c.1744C>T | p.Arg582Trp | missense_variant | 17/17 | 1 | NM_005116.6 | P1 | |
SLC23A2 | ENST00000379333.5 | c.1744C>T | p.Arg582Trp | missense_variant | 17/17 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 151992Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000897 AC: 22AN: 245262Hom.: 0 AF XY: 0.0000754 AC XY: 10AN XY: 132622
GnomAD4 exome AF: 0.000116 AC: 169AN: 1455484Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 723456
GnomAD4 genome AF: 0.000158 AC: 24AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.1744C>T (p.R582W) alteration is located in exon 17 (coding exon 15) of the SLC23A2 gene. This alteration results from a C to T substitution at nucleotide position 1744, causing the arginine (R) at amino acid position 582 to be replaced by a tryptophan (W). 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