17-1575759-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152346.3(SLC43A2):c.1555G>A(p.Val519Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,610,588 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_152346.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC43A2 | ENST00000301335.10 | c.1555G>A | p.Val519Met | missense_variant | Exon 14 of 14 | 1 | NM_152346.3 | ENSP00000301335.5 | ||
SLC43A2 | ENST00000571650.5 | c.1567G>A | p.Val523Met | missense_variant | Exon 15 of 15 | 1 | ENSP00000461382.1 | |||
SLC43A2 | ENST00000412517.3 | c.1144G>A | p.Val382Met | missense_variant | Exon 10 of 10 | 2 | ENSP00000408284.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000288 AC: 7AN: 242876Hom.: 0 AF XY: 0.0000378 AC XY: 5AN XY: 132126
GnomAD4 exome AF: 0.0000295 AC: 43AN: 1458378Hom.: 0 Cov.: 31 AF XY: 0.0000400 AC XY: 29AN XY: 725212
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1555G>A (p.V519M) alteration is located in exon 14 (coding exon 13) of the SLC43A2 gene. This alteration results from a G to A substitution at nucleotide position 1555, causing the valine (V) at amino acid position 519 to be replaced by a methionine (M). 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