chr5-139380557-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000353963.7(SLC23A1):c.473T>G(p.Leu158Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,613,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000353963.7 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC23A1 | NM_005847.5 | c.465+8T>G | splice_region_variant, intron_variant | ENST00000348729.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC23A1 | ENST00000353963.7 | c.473T>G | p.Leu158Trp | missense_variant | 5/15 | 1 | |||
SLC23A1 | ENST00000348729.8 | c.465+8T>G | splice_region_variant, intron_variant | 1 | NM_005847.5 | P1 | |||
SLC23A1 | ENST00000504513.1 | c.43+8T>G | splice_region_variant, intron_variant | 5 | |||||
SLC23A1 | ENST00000503919.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251468Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135906
GnomAD4 exome AF: 0.000174 AC: 255AN: 1461454Hom.: 0 Cov.: 31 AF XY: 0.000158 AC XY: 115AN XY: 727104
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.473T>G (p.L158W) alteration is located in exon 5 (coding exon 5) of the SLC23A1 gene. This alteration results from a T to G substitution at nucleotide position 473, causing the leucine (L) at amino acid position 158 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