17-72947834-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_139177.4(SLC39A11):c.348C>T(p.Phe116=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000233 in 1,614,082 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 2 hom. )
Consequence
SLC39A11
NM_139177.4 synonymous
NM_139177.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.72
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 17-72947834-G-A is Benign according to our data. Variant chr17-72947834-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648171.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.72 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A11 | NM_139177.4 | c.348C>T | p.Phe116= | synonymous_variant | 5/10 | ENST00000255559.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A11 | ENST00000255559.8 | c.348C>T | p.Phe116= | synonymous_variant | 5/10 | 1 | NM_139177.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000517 AC: 130AN: 251438Hom.: 1 AF XY: 0.000662 AC XY: 90AN XY: 135890
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GnomAD4 exome AF: 0.000246 AC: 360AN: 1461830Hom.: 2 Cov.: 29 AF XY: 0.000349 AC XY: 254AN XY: 727222
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GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74440
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | SLC39A11: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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