chr17-72849693-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_139177.4(SLC39A11):c.542G>A(p.Gly181Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,609,994 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_139177.4 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 |
---|---|---|---|---|---|---|---|
SLC39A11 | NM_139177.4 | c.542G>A | p.Gly181Asp | missense_variant | 6/10 | ENST00000255559.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A11 | ENST00000255559.8 | c.542G>A | p.Gly181Asp | missense_variant | 6/10 | 1 | NM_139177.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152094Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000565 AC: 14AN: 247636Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 133976
GnomAD4 exome AF: 0.0000466 AC: 68AN: 1457900Hom.: 0 Cov.: 32 AF XY: 0.0000455 AC XY: 33AN XY: 725274
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152094Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.563G>A (p.G188D) alteration is located in exon 6 (coding exon 5) of the SLC39A11 gene. This alteration results from a G to A substitution at nucleotide position 563, causing the glycine (G) at amino acid position 188 to be replaced by an aspartic acid (D). 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