17-72647598-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
Genomes: 𝑓 0.00016 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
SLC39A11
NM_139177.4 missense
NM_139177.4 missense
Scores
3
7
6
Clinical Significance
Conservation
PhyloP100: 7.44
Genes affected
SLC39A11 (HGNC:14463): (solute carrier family 39 member 11) Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to be located in Golgi apparatus; nucleus; and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.41522658).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A11 | NM_139177.4 | c.994G>A | p.Val332Ile | missense_variant | 10/10 | ENST00000255559.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A11 | ENST00000255559.8 | c.994G>A | p.Val332Ile | missense_variant | 10/10 | 1 | NM_139177.4 | P4 | |
SLC39A11 | ENST00000542342.6 | c.1015G>A | p.Val339Ile | missense_variant | 10/10 | 2 | A1 | ||
SLC39A11 | ENST00000579988.1 | n.421G>A | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152146Hom.: 0 Cov.: 31
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?
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GnomAD3 exomes AF: 0.000123 AC: 31AN: 251076Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135752
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GnomAD4 exome AF: 0.000189 AC: 276AN: 1461556Hom.: 0 Cov.: 30 AF XY: 0.000186 AC XY: 135AN XY: 727072
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GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152264Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74452
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MVP
MPC
0.52
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at