19-2732984-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144564.5(SLC39A3):c.712G>A(p.Ala238Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000337 in 1,600,224 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.
Frequency
Consequence
NM_144564.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC39A3 | NM_144564.5 | c.712G>A | p.Ala238Thr | missense_variant | 3/3 | ENST00000269740.9 | NP_653165.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A3 | ENST00000269740.9 | c.712G>A | p.Ala238Thr | missense_variant | 3/3 | 1 | NM_144564.5 | ENSP00000269740.3 | ||
ENSG00000267001 | ENST00000586572.1 | c.210+4064G>A | intron_variant | 4 | ENSP00000467958.1 | |||||
SLC39A3 | ENST00000545664.5 | c.712G>A | p.Ala238Thr | missense_variant | 3/4 | 2 | ENSP00000445345.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000389 AC: 9AN: 231348Hom.: 0 AF XY: 0.0000236 AC XY: 3AN XY: 127266
GnomAD4 exome AF: 0.0000331 AC: 48AN: 1447996Hom.: 0 Cov.: 33 AF XY: 0.0000306 AC XY: 22AN XY: 718844
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 07, 2024 | The c.712G>A (p.A238T) alteration is located in exon 3 (coding exon 2) of the SLC39A3 gene. This alteration results from a G to A substitution at nucleotide position 712, causing the alanine (A) at amino acid position 238 to be replaced by a threonine (T). 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