chr6-33201409-ACCATGGCCACAGCCATGC-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006979.3(SLC39A7):c.174_191del(p.Ser59_His64del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000889 in 1,461,818 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
SLC39A7
NM_006979.3 inframe_deletion
NM_006979.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.01
Genes affected
SLC39A7 (HGNC:4927): (solute carrier family 39 member 7) The protein encoded by this gene transports zinc from the Golgi and endoplasmic reticulum to the cytoplasm. This transport may be important for activation of tyrosine kinases, some of which could be involved in cancer progression. Therefore, modulation of the encoded protein could be useful as a therapeutic agent against cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC39A7 | NM_006979.3 | c.174_191del | p.Ser59_His64del | inframe_deletion | 1/7 | ENST00000374677.8 | NP_008910.2 | |
SLC39A7 | NM_001077516.2 | c.174_191del | p.Ser59_His64del | inframe_deletion | 2/8 | NP_001070984.1 | ||
SLC39A7 | NM_001288777.2 | c.52+31_52+48del | intron_variant | NP_001275706.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A7 | ENST00000374677.8 | c.174_191del | p.Ser59_His64del | inframe_deletion | 1/7 | 1 | NM_006979.3 | ENSP00000363809 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249580Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135406
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GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461818Hom.: 0 AF XY: 0.0000124 AC XY: 9AN XY: 727220
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 24, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals with SLC39A7-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant, c.174_191del, results in the deletion of 6 amino acid(s) of the SLC39A7 protein (p.Ser59_His64del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at