11-57489295-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003627.6(SLC43A1):c.1291G>T(p.Val431Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,614,078 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.1291G>T | p.Val431Leu | missense_variant | Exon 12 of 15 | ENST00000278426.8 | NP_003618.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC43A1 | ENST00000278426.8 | c.1291G>T | p.Val431Leu | missense_variant | Exon 12 of 15 | 1 | NM_003627.6 | ENSP00000278426.3 | ||
SLC43A1 | ENST00000528450.5 | c.1291G>T | p.Val431Leu | missense_variant | Exon 12 of 15 | 1 | ENSP00000435673.1 | |||
SLC43A1 | ENST00000525764.5 | c.398G>T | p.Cys133Phe | missense_variant | Exon 4 of 6 | 3 | ENSP00000435803.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251486Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1291G>T (p.V431L) alteration is located in exon 12 (coding exon 11) of the SLC43A1 gene. This alteration results from a G to T substitution at nucleotide position 1291, causing the valine (V) at amino acid position 431 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