chr4-41990660-C-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006345.4(SLC30A9):āc.9C>Gā(p.Pro3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 1,602,308 control chromosomes in the GnomAD database, including 532,853 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.69 ( 40037 hom., cov: 35)
Exomes š: 0.82 ( 492816 hom. )
Consequence
SLC30A9
NM_006345.4 synonymous
NM_006345.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.311
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 Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 4-41990660-C-G is Benign according to our data. Variant chr4-41990660-C-G is described in ClinVar as [Benign]. Clinvar id is 1242979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.311 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A9 | NM_006345.4 | c.9C>G | p.Pro3= | synonymous_variant | 1/18 | ENST00000264451.12 | |
SLC30A9 | XM_047449525.1 | c.9C>G | p.Pro3= | synonymous_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A9 | ENST00000264451.12 | c.9C>G | p.Pro3= | synonymous_variant | 1/18 | 1 | NM_006345.4 | P1 | |
SLC30A9 | ENST00000510460.1 | n.134C>G | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
SLC30A9 | ENST00000513699.5 | c.9C>G | p.Pro3= | synonymous_variant, NMD_transcript_variant | 1/19 | 2 |
Frequencies
GnomAD3 genomes AF: 0.689 AC: 104911AN: 152160Hom.: 40022 Cov.: 35
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GnomAD3 exomes AF: 0.810 AC: 193996AN: 239426Hom.: 80971 AF XY: 0.818 AC XY: 106963AN XY: 130762
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GnomAD4 exome AF: 0.820 AC: 1188670AN: 1450030Hom.: 492816 Cov.: 33 AF XY: 0.821 AC XY: 591673AN XY: 720240
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GnomAD4 genome AF: 0.689 AC: 104969AN: 152278Hom.: 40037 Cov.: 35 AF XY: 0.696 AC XY: 51839AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 13, 2019 | - - |
Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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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