19-49430668-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020309.4(SLC17A7):c.1534G>A(p.Gly512Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,028 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_020309.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC17A7 | ENST00000221485.8 | c.1534G>A | p.Gly512Ser | missense_variant | Exon 12 of 12 | 1 | NM_020309.4 | ENSP00000221485.2 | ||
SLC17A7 | ENST00000600601.5 | c.1333G>A | p.Gly445Ser | missense_variant | Exon 12 of 12 | 2 | ENSP00000470338.1 | |||
SLC17A7 | ENST00000600672.5 | n.*87G>A | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250536Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135682
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461866Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1534G>A (p.G512S) alteration is located in exon 12 (coding exon 12) of the SLC17A7 gene. This alteration results from a G to A substitution at nucleotide position 1534, causing the glycine (G) at amino acid position 512 to be replaced by a serine (S). 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