5-69100937-T-TG
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000396591.8(SLC30A5):c.206+17dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 148,588 control chromosomes in the GnomAD database, including 2,443 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2443 hom., cov: 26)
Exomes 𝑓: 0.14 ( 1424 hom. )
Failed GnomAD Quality Control
Consequence
SLC30A5
ENST00000396591.8 intron
ENST00000396591.8 intron
Scores
Not classified
Clinical Significance
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 Benign. Variant got -10 ACMG points.
BP6
Variant 5-69100937-T-TG is Benign according to our data. Variant chr5-69100937-T-TG is described in ClinVar as [Benign]. Clinvar id is 769300.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC30A5 | NM_022902.5 | c.206+17dup | intron_variant | ENST00000396591.8 | NP_075053.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC30A5 | ENST00000396591.8 | c.206+17dup | intron_variant | 1 | NM_022902.5 | ENSP00000379836 | P1 | |||
SLC30A5 | ENST00000380860.8 | c.206+17dup | intron_variant | 1 | ENSP00000370241 | |||||
SLC30A5 | ENST00000502979.1 | c.84-2116dup | intron_variant | 1 | ENSP00000421251 | |||||
SLC30A5 | ENST00000504103.5 | c.84-2116dup | intron_variant | 3 | ENSP00000426751 |
Frequencies
GnomAD3 genomes AF: 0.169 AC: 25102AN: 148476Hom.: 2443 Cov.: 26
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GnomAD3 exomes AF: 0.175 AC: 31354AN: 179504Hom.: 249 AF XY: 0.176 AC XY: 17327AN XY: 98396
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.144 AC: 174879AN: 1218220Hom.: 1424 Cov.: 29 AF XY: 0.143 AC XY: 86459AN XY: 604960
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.169 AC: 25097AN: 148588Hom.: 2443 Cov.: 26 AF XY: 0.166 AC XY: 12009AN XY: 72322
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 16, 2018 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at