rs2257212
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_021082.4(SLC15A2):āc.1048C>Gā(p.Leu350Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,610,042 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. 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. L350F) has been classified as Likely benign.
Frequency
Consequence
NM_021082.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC15A2 | NM_021082.4 | c.1048C>G | p.Leu350Val | missense_variant | 13/22 | ENST00000489711.6 | |
SLC15A2 | NM_001145998.2 | c.955C>G | p.Leu319Val | missense_variant | 12/21 | ||
SLC15A2 | XM_005247722.4 | c.1048C>G | p.Leu350Val | missense_variant | 13/21 | ||
SLC15A2 | XM_006713736.4 | c.1048C>G | p.Leu350Val | missense_variant | 13/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC15A2 | ENST00000489711.6 | c.1048C>G | p.Leu350Val | missense_variant | 13/22 | 1 | NM_021082.4 | P1 | |
SLC15A2 | ENST00000295605.6 | c.955C>G | p.Leu319Val | missense_variant | 12/21 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151872Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1458170Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 725674
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151872Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74148
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at