10-17961692-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145195.2(SLC39A12):c.373C>G(p.Gln125Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145195.2 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 |
---|---|---|---|---|---|---|---|
SLC39A12 | NM_001145195.2 | c.373C>G | p.Gln125Glu | missense_variant | 3/13 | ENST00000377369.7 | |
SLC39A12 | NM_001282733.2 | c.373C>G | p.Gln125Glu | missense_variant | 3/13 | ||
SLC39A12 | NM_152725.4 | c.373C>G | p.Gln125Glu | missense_variant | 3/12 | ||
SLC39A12 | NM_001282734.2 | c.-30C>G | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A12 | ENST00000377369.7 | c.373C>G | p.Gln125Glu | missense_variant | 3/13 | 1 | NM_001145195.2 | A1 | |
SLC39A12 | ENST00000377371.3 | c.373C>G | p.Gln125Glu | missense_variant | 3/13 | 1 | P4 | ||
SLC39A12 | ENST00000377374.8 | c.373C>G | p.Gln125Glu | missense_variant | 3/12 | 2 | |||
SLC39A12 | ENST00000539911.5 | c.-30C>G | 5_prime_UTR_variant | 2/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251226Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135784
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461688Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727160
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.373C>G (p.Q125E) alteration is located in exon 3 (coding exon 2) of the SLC39A12 gene. This alteration results from a C to G substitution at nucleotide position 373, causing the glutamine (Q) at amino acid position 125 to be replaced by a glutamic acid (E). 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