chr11-57407885-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_199329.3(SLC43A3):c.1383G>A(p.Met461Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000892 in 1,457,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_199329.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC43A3 | NM_199329.3 | c.1383G>A | p.Met461Ile | missense_variant | Exon 14 of 14 | ENST00000395124.6 | NP_955361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC43A3 | ENST00000395124.6 | c.1383G>A | p.Met461Ile | missense_variant | Exon 14 of 14 | 1 | NM_199329.3 | ENSP00000378556.1 | ||
ENSG00000254979 | ENST00000529411.1 | c.303+1290G>A | intron_variant | Intron 2 of 3 | 4 | ENSP00000431536.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251278Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135802
GnomAD4 exome AF: 0.00000892 AC: 13AN: 1457890Hom.: 0 Cov.: 28 AF XY: 0.00000413 AC XY: 3AN XY: 725590
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1383G>A (p.M461I) alteration is located in exon 14 (coding exon 12) of the SLC43A3 gene. This alteration results from a G to A substitution at nucleotide position 1383, causing the methionine (M) at amino acid position 461 to be replaced by an isoleucine (I). 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