chr11-47408641-T-TCGC
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001128225.3(SLC39A13):c.-14_-12dupCGC variant causes a splice region change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 6896 hom., cov: 0)
Exomes 𝑓: 0.41 ( 110 hom. )
Consequence
SLC39A13
NM_001128225.3 splice_region
NM_001128225.3 splice_region
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.167
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 -10 ACMG points.
BP6
Variant 11-47408641-T-TCGC is Benign according to our data. Variant chr11-47408641-T-TCGC is described in ClinVar as [Benign]. Clinvar id is 517012.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC39A13 | NM_001128225.3 | c.-14_-12dupCGC | splice_region_variant | 1/10 | ENST00000362021.9 | NP_001121697.2 | ||
SLC39A13 | NM_001128225.3 | c.-14_-12dupCGC | 5_prime_UTR_variant | 1/10 | ENST00000362021.9 | NP_001121697.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A13 | ENST00000362021.9 | c.-14_-12dupCGC | splice_region_variant | 1/10 | 1 | NM_001128225.3 | ENSP00000354689.4 | |||
SLC39A13 | ENST00000362021.9 | c.-14_-12dupCGC | 5_prime_UTR_variant | 1/10 | 1 | NM_001128225.3 | ENSP00000354689.4 |
Frequencies
GnomAD3 genomes AF: 0.300 AC: 44648AN: 148598Hom.: 6881 Cov.: 0
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GnomAD4 exome AF: 0.410 AC: 548AN: 1338Hom.: 110 Cov.: 0 AF XY: 0.416 AC XY: 349AN XY: 838
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GnomAD4 genome AF: 0.301 AC: 44687AN: 148700Hom.: 6896 Cov.: 0 AF XY: 0.301 AC XY: 21852AN XY: 72498
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 30, 2018 | - - |
Benign, flagged submission | clinical testing | GeneDx | Sep 30, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at