rs73924411
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000233535.9(SLC30A3):c.884-115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0482 in 1,435,532 control chromosomes in the GnomAD database, including 1,850 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 0.056 ( 267 hom., cov: 32)
Exomes 𝑓: 0.047 ( 1583 hom. )
Consequence
SLC30A3
ENST00000233535.9 intron
ENST00000233535.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.203
Genes affected
SLC30A3 (HGNC:11014): (solute carrier family 30 member 3) Predicted to enable zinc ion transmembrane transporter activity. Involved in regulation of sequestering of zinc ion. Located in late endosome and synaptic vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC30A3 | NM_003459.5 | c.884-115G>A | intron_variant | ENST00000233535.9 | NP_003450.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC30A3 | ENST00000233535.9 | c.884-115G>A | intron_variant | 1 | NM_003459.5 | ENSP00000233535 | P1 | |||
SLC30A3 | ENST00000445870.5 | c.695-115G>A | intron_variant | 5 | ENSP00000388219 | |||||
SLC30A3 | ENST00000482990.1 | n.774-115G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
SLC30A3 | ENST00000497341.5 | n.1537-115G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0556 AC: 8453AN: 152076Hom.: 267 Cov.: 32
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GnomAD4 exome AF: 0.0473 AC: 60721AN: 1283338Hom.: 1583 Cov.: 18 AF XY: 0.0478 AC XY: 30561AN XY: 639032
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GnomAD4 genome AF: 0.0555 AC: 8449AN: 152194Hom.: 267 Cov.: 32 AF XY: 0.0540 AC XY: 4016AN XY: 74416
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at