chr4-42001818-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006345.4(SLC30A9):c.274+38C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,444,750 control chromosomes in the GnomAD database, including 431,304 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.64 ( 35590 hom., cov: 31)
Exomes 𝑓: 0.78 ( 395714 hom. )
Consequence
SLC30A9
NM_006345.4 intron
NM_006345.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.08
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 4-42001818-C-G is Benign according to our data. Variant chr4-42001818-C-G is described in ClinVar as [Benign]. Clinvar id is 1333131.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A9 | NM_006345.4 | c.274+38C>G | intron_variant | ENST00000264451.12 | |||
SLC30A9 | XM_047449525.1 | c.274+38C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A9 | ENST00000264451.12 | c.274+38C>G | intron_variant | 1 | NM_006345.4 | P1 | |||
SLC30A9 | ENST00000513699.5 | c.274+38C>G | intron_variant, NMD_transcript_variant | 2 | |||||
SLC30A9 | ENST00000510460.1 | n.399+38C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.638 AC: 96807AN: 151724Hom.: 35581 Cov.: 31
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GnomAD3 exomes AF: 0.771 AC: 157657AN: 204508Hom.: 62867 AF XY: 0.777 AC XY: 86874AN XY: 111738
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GnomAD4 exome AF: 0.777 AC: 1004152AN: 1292908Hom.: 395714 Cov.: 17 AF XY: 0.777 AC XY: 504699AN XY: 649334
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GnomAD4 genome ? AF: 0.638 AC: 96836AN: 151842Hom.: 35590 Cov.: 31 AF XY: 0.646 AC XY: 47974AN XY: 74268
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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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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