NM_003627.6:c.1498G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003627.6(SLC43A1):c.1498G>A(p.Ala500Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003627.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC43A1 | NM_003627.6 | c.1498G>A | p.Ala500Thr | missense_variant | Exon 14 of 15 | ENST00000278426.8 | NP_003618.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC43A1 | ENST00000278426.8 | c.1498G>A | p.Ala500Thr | missense_variant | Exon 14 of 15 | 1 | NM_003627.6 | ENSP00000278426.3 | ||
SLC43A1 | ENST00000528450.5 | c.1498G>A | p.Ala500Thr | missense_variant | Exon 14 of 15 | 1 | ENSP00000435673.1 | |||
SLC43A1 | ENST00000525764.5 | c.*50G>A | downstream_gene_variant | 3 | ENSP00000435803.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251332Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135860
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727200
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1498G>A (p.A500T) alteration is located in exon 14 (coding exon 13) of the SLC43A1 gene. This alteration results from a G to A substitution at nucleotide position 1498, causing the alanine (A) at amino acid position 500 to be replaced by a threonine (T). 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