19-46777293-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005628.3(SLC1A5):c.1171G>A(p.Ala391Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005628.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC1A5 | NM_005628.3 | c.1171G>A | p.Ala391Thr | missense_variant | Exon 6 of 8 | ENST00000542575.6 | NP_005619.1 | |
SLC1A5 | NM_001145145.2 | c.565G>A | p.Ala189Thr | missense_variant | Exon 5 of 7 | NP_001138617.1 | ||
SLC1A5 | NM_001145144.2 | c.487G>A | p.Ala163Thr | missense_variant | Exon 6 of 8 | NP_001138616.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461438Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727040
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1171G>A (p.A391T) alteration is located in exon 6 (coding exon 6) of the SLC1A5 gene. This alteration results from a G to A substitution at nucleotide position 1171, causing the alanine (A) at amino acid position 391 to be replaced by a threonine (T). 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