chr17-72648903-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_139177.4(SLC39A11):c.829G>A(p.Val277Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000397 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A11 | ENST00000255559.8 | c.829G>A | p.Val277Met | missense_variant | Exon 9 of 10 | 1 | NM_139177.4 | ENSP00000255559.3 | ||
SLC39A11 | ENST00000542342.6 | c.850G>A | p.Val284Met | missense_variant | Exon 9 of 10 | 2 | ENSP00000445829.2 | |||
SLC39A11 | ENST00000579988.1 | n.256G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 3 | |||||
SLC39A11 | ENST00000582769.5 | c.*20G>A | downstream_gene_variant | 5 | ENSP00000463467.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000877 AC: 22AN: 250878Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135688
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461790Hom.: 0 Cov.: 32 AF XY: 0.0000330 AC XY: 24AN XY: 727192
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.850G>A (p.V284M) alteration is located in exon 9 (coding exon 8) of the SLC39A11 gene. This alteration results from a G to A substitution at nucleotide position 850, causing the valine (V) at amino acid position 284 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