4-41990702-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006345.4(SLC30A9):c.51C>T(p.Ser17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,612,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000058 ( 0 hom. )
Consequence
SLC30A9
NM_006345.4 synonymous
NM_006345.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.38
Genes affected
SLC30A9 (HGNC:1329): (solute carrier family 30 member 9) Predicted to enable nuclear receptor coactivator activity. Involved in cellular zinc ion homeostasis and zinc ion transport. Located in several cellular components, including cytoplasmic vesicle; cytoskeleton; and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 4-41990702-C-T is Benign according to our data. Variant chr4-41990702-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3053487.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.38 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A9 | NM_006345.4 | c.51C>T | p.Ser17= | synonymous_variant | 1/18 | ENST00000264451.12 | |
SLC30A9 | XM_047449525.1 | c.51C>T | p.Ser17= | synonymous_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A9 | ENST00000264451.12 | c.51C>T | p.Ser17= | synonymous_variant | 1/18 | 1 | NM_006345.4 | P1 | |
SLC30A9 | ENST00000510460.1 | n.176C>T | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
SLC30A9 | ENST00000513699.5 | c.51C>T | p.Ser17= | synonymous_variant, NMD_transcript_variant | 1/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152250Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000695 AC: 17AN: 244742Hom.: 0 AF XY: 0.0000822 AC XY: 11AN XY: 133748
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GnomAD4 exome AF: 0.0000575 AC: 84AN: 1460022Hom.: 0 Cov.: 33 AF XY: 0.0000551 AC XY: 40AN XY: 726254
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GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74510
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC30A9-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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