1-153960439-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001271958.2(SLC39A1):c.634C>A(p.Leu212Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,461,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001271958.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A1 | NM_001271958.2 | c.634C>A | p.Leu212Met | missense_variant | 4/4 | ENST00000356205.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A1 | ENST00000356205.9 | c.634C>A | p.Leu212Met | missense_variant | 4/4 | 1 | NM_001271958.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250444Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135588
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461566Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727102
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.634C>A (p.L212M) alteration is located in exon 5 (coding exon 3) of the SLC39A1 gene. This alteration results from a C to A substitution at nucleotide position 634, causing the leucine (L) at amino acid position 212 to be replaced by a methionine (M). 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