chr17-73031663-C-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_139177.4(SLC39A11):c.199G>T(p.Ala67Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000651 in 1,614,116 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 0.00035 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
SLC39A11
NM_139177.4 missense
NM_139177.4 missense
Scores
5
12
Clinical Significance
Conservation
PhyloP100: 7.07
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.030735075).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A11 | NM_139177.4 | c.199G>T | p.Ala67Ser | missense_variant | 4/10 | ENST00000255559.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A11 | ENST00000255559.8 | c.199G>T | p.Ala67Ser | missense_variant | 4/10 | 1 | NM_139177.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000348 AC: 53AN: 152148Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000119 AC: 30AN: 251346Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135848
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GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727224
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GnomAD4 genome AF: 0.000348 AC: 53AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74468
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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 | Sep 26, 2023 | The c.199G>T (p.A67S) alteration is located in exon 4 (coding exon 3) of the SLC39A11 gene. This alteration results from a G to T substitution at nucleotide position 199, causing the alanine (A) at amino acid position 67 to be replaced by a serine (S). 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
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;.;.
REVEL
Benign
Sift
Benign
T;T;.;.;.
Sift4G
Benign
T;T;T;.;.
Polyphen
D;D;.;.;.
Vest4
MVP
MPC
0.57
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at