rs3019885
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000521243.5(SLC30A8):c.-107+62287T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
SLC30A8
ENST00000521243.5 intron
ENST00000521243.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.556
Genes affected
SLC30A8 (HGNC:20303): (solute carrier family 30 member 8) The protein encoded by this gene is a zinc efflux transporter involved in the accumulation of zinc in intracellular vesicles. This gene is expressed at a high level only in the pancreas, particularly in islets of Langerhans. The encoded protein colocalizes with insulin in the secretory pathway granules of the insulin-secreting INS-1 cells. Allelic variants of this gene exist that confer susceptibility to diabetes mellitus, noninsulin-dependent (NIDDM). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC30A8 | NM_001172811.2 | c.-107+62287T>A | intron_variant | NP_001166282.1 | ||||
SLC30A8 | NM_001172813.2 | c.-274+6293T>A | intron_variant | NP_001166284.1 | ||||
SLC30A8 | NM_001172815.3 | c.-265-25813T>A | intron_variant | NP_001166286.1 | ||||
SLC30A8 | XM_024447083.2 | c.-107+62287T>A | intron_variant | XP_024302851.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC30A8 | ENST00000521243.5 | c.-107+62287T>A | intron_variant | 1 | ENSP00000428545 | |||||
SLC30A8 | ENST00000427715.2 | c.-265-25813T>A | intron_variant | 2 | ENSP00000407505 | |||||
SLC30A8 | ENST00000524274.5 | c.-107+62287T>A | intron_variant | 4 | ENSP00000427760 | |||||
SLC30A8 | ENST00000521035.5 | n.294+6293T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at