chr11-119024913-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The ENST00000330775.9(SLC37A4):c.1287G>A(p.Glu429=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,272 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: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SLC37A4
ENST00000330775.9 synonymous
ENST00000330775.9 synonymous
Scores
1
1
11
Clinical Significance
Conservation
PhyloP100: 1.33
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 Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.11344403).
BP6
?
Variant 11-119024913-C-T is Benign according to our data. Variant chr11-119024913-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2902343.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.33 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC37A4 | NM_001164277.2 | c.1287G>A | p.Glu429= | synonymous_variant | 11/11 | ENST00000642844.3 | |
SLC37A4 | NM_001164279.2 | c.1068G>A | p.Glu356= | synonymous_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC37A4 | ENST00000330775.9 | c.1287G>A | p.Glu429= | synonymous_variant | 10/10 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248200Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134688
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461272Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726862
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GnomAD4 genome ? Cov.: 33
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Cov.:
33
Bravo
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glucose-6-phosphate transport defect Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 26, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Vest4
MutPred
Gain of sheet (P = 0.0085);
MVP
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at