rs2071225
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000169.3(GLA):c.-10C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 1,201,243 control chromosomes in the GnomAD database, including 2,804 homozygotes. There are 31,097 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.070 ( 208 hom., 2527 hem., cov: 23)
Exomes 𝑓: 0.074 ( 2596 hom. 28570 hem. )
Consequence
GLA
NM_000169.3 5_prime_UTR
NM_000169.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.554
Genes affected
GLA (HGNC:4296): (galactosidase alpha) This gene encodes a homodimeric glycoprotein that hydrolyses the terminal alpha-galactosyl moieties from glycolipids and glycoproteins. This enzyme predominantly hydrolyzes ceramide trihexoside, and it can catalyze the hydrolysis of melibiose into galactose and glucose. A variety of mutations in this gene affect the synthesis, processing, and stability of this enzyme, which causes Fabry disease, a rare lysosomal storage disorder that results from a failure to catabolize alpha-D-galactosyl glycolipid moieties. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant X-101407913-G-A is Benign according to our data. Variant chrX-101407913-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 36280.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-101407913-G-A is described in Lovd as [Benign]. Variant chrX-101407913-G-A is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLA | NM_000169.3 | c.-10C>T | 5_prime_UTR_variant | 1/7 | ENST00000218516.4 | ||
RPL36A-HNRNPH2 | NM_001199973.2 | c.301-4023G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLA | ENST00000218516.4 | c.-10C>T | 5_prime_UTR_variant | 1/7 | 1 | NM_000169.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0700 AC: 7839AN: 111984Hom.: 209 Cov.: 23 AF XY: 0.0739 AC XY: 2524AN XY: 34166
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GnomAD3 exomes AF: 0.0932 AC: 17056AN: 182908Hom.: 754 AF XY: 0.0995 AC XY: 6711AN XY: 67418
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GnomAD4 exome AF: 0.0736 AC: 80193AN: 1089205Hom.: 2596 Cov.: 31 AF XY: 0.0804 AC XY: 28570AN XY: 355297
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GnomAD4 genome ? AF: 0.0699 AC: 7833AN: 112038Hom.: 208 Cov.: 23 AF XY: 0.0738 AC XY: 2527AN XY: 34230
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:18
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:6
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 12, 2013 | -10C>T in 5'UTR of GLA: This variant is not expected to have clinical significan ce because it has been identified in 6.7% (256/3835) of African American chromos omes from a broad population by the NHLBI Exome Sequencing Project (http://evs.g s.washington.edu/EVS/; dbSNP rs2071225). -10C>T in 5'UTR of GLA (rs2071225; all ele frequency = 6.7%, 256/3835) ** - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 06, 2018 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Fabry disease Benign:5
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Mar 19, 2018 | - - |
not provided Benign:5
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 14, 2020 | This variant is associated with the following publications: (PMID: 21092187, 21896204, 18979223, 26981927, 25281798, 26334996, 25772321, 23677059, 22682330, 21683120, 8411052, 26070511, 29794742, 31996269) - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 19, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 28, 2023 | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 15, 2015 | - - |
Cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 18, 2011 | - - |
Hypertrophic cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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