rs9302952
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_139177.4(SLC39A11):c.147+16721T>G variant causes a intron change. The variant allele was found at a frequency of 0.145 in 1,458,076 control chromosomes in the GnomAD database, including 16,250 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 1523 hom., cov: 31)
Exomes 𝑓: 0.15 ( 14727 hom. )
Consequence
SLC39A11
NM_139177.4 intron
NM_139177.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.80
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A11 | NM_139177.4 | c.147+16721T>G | intron_variant | ENST00000255559.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A11 | ENST00000255559.8 | c.147+16721T>G | intron_variant | 1 | NM_139177.4 | P4 | |||
ATG12P1 | ENST00000578331.1 | n.202T>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.139 AC: 21107AN: 151804Hom.: 1525 Cov.: 31
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GnomAD4 exome AF: 0.146 AC: 190180AN: 1306154Hom.: 14727 Cov.: 25 AF XY: 0.144 AC XY: 94826AN XY: 657896
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GnomAD4 genome ? AF: 0.139 AC: 21112AN: 151922Hom.: 1523 Cov.: 31 AF XY: 0.136 AC XY: 10110AN XY: 74236
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at