rs397840868
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022902.5(SLC30A5):c.206+17delG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00381 in 1,383,500 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0043 ( 0 hom. )
Consequence
SLC30A5
NM_022902.5 intron
NM_022902.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.402
Genes affected
SLC30A5 (HGNC:19089): (solute carrier family 30 member 5) This gene encodes a member of the SLC30A/ZnT family of zinc transporter proteins. ZnT proteins mediate both cellular zinc efflux and zinc sequestration into membrane-bound organelles. The encoded protein plays a role in the early secretory pathway as a heterodimer with zinc transporter 6, and may also regulate zinc sequestration into secretory granules of pancreatic beta cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 19. [provided by RefSeq, Oct 2011]
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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
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC30A5 | ENST00000396591.8 | c.206+9delG | intron_variant | Intron 2 of 15 | 1 | NM_022902.5 | ENSP00000379836.3 | |||
| SLC30A5 | ENST00000380860.8 | c.206+9delG | intron_variant | Intron 2 of 3 | 1 | ENSP00000370241.4 | ||||
| SLC30A5 | ENST00000502979.1 | c.84-2124delG | intron_variant | Intron 1 of 2 | 1 | ENSP00000421251.1 | ||||
| SLC30A5 | ENST00000504103.5 | c.84-2124delG | intron_variant | Intron 1 of 2 | 3 | ENSP00000426751.1 |
Frequencies
GnomAD3 genomes 0.0000268 AC: 4AN: 149014Hom.: 0 Cov.: 26
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GnomAD3 exomes AF: 0.00328 AC: 588AN: 179504Hom.: 0 AF XY: 0.00316 AC XY: 311AN XY: 98396
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GnomAD4 exome AF: 0.00426 AC: 5262AN: 1234374Hom.: 0 Cov.: 29 AF XY: 0.00439 AC XY: 2689AN XY: 612836
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GnomAD4 genome 0.0000268 AC: 4AN: 149126Hom.: 0 Cov.: 26 AF XY: 0.0000413 AC XY: 3AN XY: 72606
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at