rs746808726
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033409.4(SLC52A3):c.31G>C(p.Val11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,611,070 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V11A) has been classified as Uncertain significance.
Frequency
Consequence
NM_033409.4 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 |
---|---|---|---|---|---|---|---|
SLC52A3 | NM_033409.4 | c.31G>C | p.Val11Leu | missense_variant | 2/5 | ENST00000645534.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC52A3 | ENST00000645534.1 | c.31G>C | p.Val11Leu | missense_variant | 2/5 | NM_033409.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000668 AC: 1AN: 149726Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246332Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133568
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461344Hom.: 0 Cov.: 36 AF XY: 0.00000688 AC XY: 5AN XY: 726944
GnomAD4 genome ? AF: 0.00000668 AC: 1AN: 149726Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1AN XY: 73148
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at