chr17-28491461-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003984.4(SLC13A2):c.599C>T(p.Thr200Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,613,710 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_003984.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC13A2 | NM_003984.4 | c.599C>T | p.Thr200Met | missense_variant | 5/12 | ENST00000314669.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC13A2 | ENST00000314669.10 | c.599C>T | p.Thr200Met | missense_variant | 5/12 | 1 | NM_003984.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250828Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135736
GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461342Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 726998
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.746C>T (p.T249M) alteration is located in exon 5 (coding exon 5) of the SLC13A2 gene. This alteration results from a C to T substitution at nucleotide position 746, causing the threonine (T) at amino acid position 249 to be replaced by a methionine (M). 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