11-57485169-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003627.6(SLC43A1):c.1607G>A(p.Arg536Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R536W) has been classified as Uncertain significance.
Frequency
Consequence
NM_003627.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC43A1 | NM_003627.6 | c.1607G>A | p.Arg536Gln | missense_variant | Exon 15 of 15 | ENST00000278426.8 | NP_003618.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC43A1 | ENST00000278426.8 | c.1607G>A | p.Arg536Gln | missense_variant | Exon 15 of 15 | 1 | NM_003627.6 | ENSP00000278426.3 | ||
SLC43A1 | ENST00000528450.5 | c.1607G>A | p.Arg536Gln | missense_variant | Exon 15 of 15 | 1 | ENSP00000435673.1 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152086Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251128Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135796
GnomAD4 exome AF: 0.000127 AC: 185AN: 1461832Hom.: 0 Cov.: 30 AF XY: 0.000120 AC XY: 87AN XY: 727214
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1607G>A (p.R536Q) alteration is located in exon 15 (coding exon 14) of the SLC43A1 gene. This alteration results from a G to A substitution at nucleotide position 1607, causing the arginine (R) at amino acid position 536 to be replaced by a glutamine (Q). 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