11-119024841-CCTT-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000330775.9(SLC37A4):c.*66_*68del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000645 in 1,550,158 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Consequence
SLC37A4
ENST00000330775.9 3_prime_UTR
ENST00000330775.9 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0830
Genes affected
SLC37A4 (HGNC:4061): (solute carrier family 37 member 4) This gene regulates glucose-6-phosphate transport from the cytoplasm to the lumen of the endoplasmic reticulum, in order to maintain glucose homeostasis. It also plays a role in ATP-mediated calcium sequestration in the lumen of the endoplasmic reticulum. Mutations in this gene have been associated with various forms of glycogen storage disease. Alternative splicing in this gene results in multiple transcript variants.[provided by RefSeq, Aug 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC37A4 | NM_001164277.2 | c.*66_*68del | 3_prime_UTR_variant | 11/11 | ENST00000642844.3 | ||
SLC37A4 | NM_001164279.2 | c.*66_*68del | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC37A4 | ENST00000330775.9 | c.*66_*68del | 3_prime_UTR_variant | 10/10 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152248Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00000509 AC: 1AN: 196430Hom.: 0 AF XY: 0.00000946 AC XY: 1AN XY: 105662
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GnomAD4 exome AF: 0.00000429 AC: 6AN: 1397910Hom.: 0 AF XY: 0.00000288 AC XY: 2AN XY: 694162
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152248Hom.: 1 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74386
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 15, 2022 | Variant summary: SLC37A4 c.*66_*68delAAG is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 5.1e-06 in 196430 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.*66_*68delAAG in individuals affected with Glycogen Storage Disease Type Ib and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at