chr17-72647598-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_139177.4(SLC39A11):c.994G>A(p.Val332Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 1,613,820 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.994G>A | p.Val332Ile | missense_variant | Exon 10 of 10 | 1 | NM_139177.4 | ENSP00000255559.3 | ||
SLC39A11 | ENST00000542342.6 | c.1015G>A | p.Val339Ile | missense_variant | Exon 10 of 10 | 2 | ENSP00000445829.2 | |||
SLC39A11 | ENST00000579988.1 | n.421G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251076Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135752
GnomAD4 exome AF: 0.000189 AC: 276AN: 1461556Hom.: 0 Cov.: 30 AF XY: 0.000186 AC XY: 135AN XY: 727072
GnomAD4 genome AF: 0.000158 AC: 24AN: 152264Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1015G>A (p.V339I) alteration is located in exon 10 (coding exon 9) of the SLC39A11 gene. This alteration results from a G to A substitution at nucleotide position 1015, causing the valine (V) at amino acid position 339 to be replaced by an isoleucine (I). 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