rs7002176
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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.830-1223T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,774 control chromosomes in the GnomAD database, including 13,211 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 0.41 ( 13211 hom., cov: 31)
Consequence
SLC30A8
NM_173851.3 intron
NM_173851.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.308
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=-0.8).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A8 | NM_173851.3 | c.830-1223T>A | intron_variant | ENST00000456015.7 | |||
LOC105375716 | XR_007061067.1 | n.819+2804A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A8 | ENST00000456015.7 | c.830-1223T>A | intron_variant | 1 | NM_173851.3 | P1 | |||
SLC30A8 | ENST00000519688.5 | c.683-1223T>A | intron_variant | 1 | |||||
SLC30A8 | ENST00000521243.5 | c.683-1223T>A | intron_variant | 1 | |||||
SLC30A8 | ENST00000427715.2 | c.683-1223T>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.406 AC: 61586AN: 151656Hom.: 13196 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.406 AC: 61641AN: 151774Hom.: 13211 Cov.: 31 AF XY: 0.404 AC XY: 29931AN XY: 74128
GnomAD4 genome
?
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31
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74128
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1457
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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