20-4884757-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005116.6(SLC23A2):c.638G>A(p.Arg213Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000448 in 1,608,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC23A2 | NM_005116.6 | c.638G>A | p.Arg213Gln | missense_variant | Exon 8 of 17 | ENST00000338244.6 | NP_005107.4 | |
SLC23A2 | NM_203327.2 | c.638G>A | p.Arg213Gln | missense_variant | Exon 8 of 17 | NP_976072.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000759 AC: 19AN: 250168Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135228
GnomAD4 exome AF: 0.0000419 AC: 61AN: 1456530Hom.: 0 Cov.: 28 AF XY: 0.0000414 AC XY: 30AN XY: 724994
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.638G>A (p.R213Q) alteration is located in exon 8 (coding exon 6) of the SLC23A2 gene. This alteration results from a G to A substitution at nucleotide position 638, causing the arginine (R) at amino acid position 213 to be replaced by a glutamine (Q). 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