19-46775673-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005628.3(SLC1A5):c.1463G>A(p.Arg488His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,090 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_005628.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC1A5 | NM_005628.3 | c.1463G>A | p.Arg488His | missense_variant | Exon 8 of 8 | ENST00000542575.6 | NP_005619.1 | |
SLC1A5 | NM_001145145.2 | c.857G>A | p.Arg286His | missense_variant | Exon 7 of 7 | NP_001138617.1 | ||
SLC1A5 | NM_001145144.2 | c.779G>A | p.Arg260His | missense_variant | Exon 8 of 8 | NP_001138616.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152100Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 249864Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135188
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461872Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 727234
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74400
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1463G>A (p.R488H) alteration is located in exon 8 (coding exon 8) of the SLC1A5 gene. This alteration results from a G to A substitution at nucleotide position 1463, causing the arginine (R) at amino acid position 488 to be replaced by a histidine (H). 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