rs11558471
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173851.3(SLC30A8):c.*813A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,070 control chromosomes in the GnomAD database, including 5,838 homozygotes. 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: 𝑓 0.25 ( 5835 hom., cov: 33)
Exomes 𝑓: 0.26 ( 3 hom. )
Consequence
SLC30A8
NM_173851.3 3_prime_UTR
NM_173851.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0970
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A8 | NM_173851.3 | c.*813A>G | 3_prime_UTR_variant | 8/8 | ENST00000456015.7 | ||
LOC105375716 | XR_007061067.1 | n.560-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A8 | ENST00000456015.7 | c.*813A>G | 3_prime_UTR_variant | 8/8 | 1 | NM_173851.3 | P1 | ||
SLC30A8 | ENST00000519688.5 | c.*813A>G | 3_prime_UTR_variant | 9/9 | 1 | ||||
SLC30A8 | ENST00000427715.2 | c.*813A>G | 3_prime_UTR_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38550AN: 151920Hom.: 5832 Cov.: 33
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GnomAD4 exome AF: 0.265 AC: 9AN: 34Hom.: 3 Cov.: 0 AF XY: 0.250 AC XY: 6AN XY: 24
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GnomAD4 genome ? AF: 0.254 AC: 38562AN: 152036Hom.: 5835 Cov.: 33 AF XY: 0.259 AC XY: 19208AN XY: 74292
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ClinVar
Not reported inComputational 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