6-25798907-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005074.5(SLC17A1):c.1282G>A(p.Ala428Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,426,184 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_005074.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC17A1 | NM_005074.5 | c.1282G>A | p.Ala428Thr | missense_variant | 12/13 | ENST00000244527.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC17A1 | ENST00000244527.10 | c.1282G>A | p.Ala428Thr | missense_variant | 12/13 | 5 | NM_005074.5 | P1 | |
SLC17A1 | ENST00000468082.1 | c.1120G>A | p.Ala374Thr | missense_variant | 10/10 | 1 | |||
SLC17A1 | ENST00000476801.5 | c.1282G>A | p.Ala428Thr | missense_variant | 12/12 | 2 | P1 | ||
SLC17A1 | ENST00000377886.6 | c.*533G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/12 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247906Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133982
GnomAD4 exome AF: 0.0000112 AC: 16AN: 1426184Hom.: 0 Cov.: 31 AF XY: 0.00000851 AC XY: 6AN XY: 704814
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.1282G>A (p.A428T) alteration is located in exon 12 (coding exon 11) of the SLC17A1 gene. This alteration results from a G to A substitution at nucleotide position 1282, causing the alanine (A) at amino acid position 428 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