12-101157319-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145913.5(SLC5A8):c.1793A>T(p.Asn598Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000253 in 1,461,354 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 (★).
Frequency
Consequence
NM_145913.5 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 |
---|---|---|---|---|---|---|---|
SLC5A8 | NM_145913.5 | c.1793A>T | p.Asn598Ile | missense_variant | 15/15 | ENST00000536262.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A8 | ENST00000536262.3 | c.1793A>T | p.Asn598Ile | missense_variant | 15/15 | 1 | NM_145913.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250914Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135616
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461354Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726958
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.1793A>T (p.N598I) alteration is located in exon 15 (coding exon 15) of the SLC5A8 gene. This alteration results from a A to T substitution at nucleotide position 1793, causing the asparagine (N) at amino acid position 598 to be replaced by an isoleucine (I). 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