rs2293576
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001128225.3(SLC39A13):c.573G>A(p.Ala191=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,613,866 control chromosomes in the GnomAD database, including 87,445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.25 ( 5897 hom., cov: 33)
Exomes 𝑓: 0.33 ( 81548 hom. )
Consequence
SLC39A13
NM_001128225.3 synonymous
NM_001128225.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.557
Genes affected
SLC39A13 (HGNC:20859): (solute carrier family 39 member 13) This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndrome. Alternate transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 11-47413435-G-A is Benign according to our data. Variant chr11-47413435-G-A is described in ClinVar as [Benign]. Clinvar id is 384707.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-47413435-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.557 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A13 | NM_001128225.3 | c.573G>A | p.Ala191= | synonymous_variant | 5/10 | ENST00000362021.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A13 | ENST00000362021.9 | c.573G>A | p.Ala191= | synonymous_variant | 5/10 | 1 | NM_001128225.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.249 AC: 37789AN: 152046Hom.: 5899 Cov.: 33
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GnomAD3 exomes AF: 0.310 AC: 77694AN: 250940Hom.: 13532 AF XY: 0.325 AC XY: 44106AN XY: 135754
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GnomAD4 exome AF: 0.327 AC: 478352AN: 1461700Hom.: 81548 Cov.: 57 AF XY: 0.332 AC XY: 241608AN XY: 727170
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GnomAD4 genome ? AF: 0.248 AC: 37780AN: 152166Hom.: 5897 Cov.: 33 AF XY: 0.248 AC XY: 18424AN XY: 74376
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 25, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 30, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Ehlers-Danlos syndrome, spondylocheirodysplastic type Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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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