11-26681123-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_178498.4(SLC5A12):c.1407G>C(p.Leu469Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000255 in 1,611,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 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 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A12 | ENST00000396005.8 | c.1407G>C | p.Leu469Phe | missense_variant | Exon 12 of 15 | 1 | NM_178498.4 | ENSP00000379326.3 | ||
SLC5A12 | ENST00000527405.5 | n.*13G>C | non_coding_transcript_exon_variant | Exon 12 of 15 | 2 | ENSP00000436011.1 | ||||
SLC5A12 | ENST00000527405.5 | n.*13G>C | 3_prime_UTR_variant | Exon 12 of 15 | 2 | ENSP00000436011.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000608 AC: 15AN: 246844Hom.: 0 AF XY: 0.0000597 AC XY: 8AN XY: 133946
GnomAD4 exome AF: 0.000274 AC: 400AN: 1459070Hom.: 0 Cov.: 34 AF XY: 0.000263 AC XY: 191AN XY: 725798
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1407G>C (p.L469F) alteration is located in exon 12 (coding exon 12) of the SLC5A12 gene. This alteration results from a G to C substitution at nucleotide position 1407, causing the leucine (L) at amino acid position 469 to be replaced by a phenylalanine (F). 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