11-26686492-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_178498.4(SLC5A12):c.1206G>T(p.Met402Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,738 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178498.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A12 | ENST00000396005.8 | c.1206G>T | p.Met402Ile | missense_variant | Exon 10 of 15 | 1 | NM_178498.4 | ENSP00000379326.3 | ||
SLC5A12 | ENST00000527405.5 | n.646G>T | non_coding_transcript_exon_variant | Exon 10 of 15 | 2 | ENSP00000436011.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249438Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135324
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461738Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727174
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1206G>T (p.M402I) alteration is located in exon 10 (coding exon 10) of the SLC5A12 gene. This alteration results from a G to T substitution at nucleotide position 1206, causing the methionine (M) at amino acid position 402 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