Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_014845.6(FIG4):c.834A>T(p.Lys278Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000219 in 1,613,222 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
FIG4 (HGNC:16873): (FIG4 phosphoinositide 5-phosphatase) The protein encoded by this gene belongs to the SAC domain-containing protein gene family. The SAC domain, approximately 400 amino acids in length and consisting of seven conserved motifs, has been shown to possess phosphoinositide phosphatase activity. The yeast homolog, Sac1p, is involved in the regulation of various phosphoinositides, and affects diverse cellular functions such as actin cytoskeleton organization, Golgi function, and maintenance of vacuole morphology. Membrane-bound phosphoinositides function as signaling molecules and play a key role in vesicle trafficking in eukaryotic cells. Mutations in this gene have been associated with Charcot-Marie-Tooth disease, type 4J. [provided by RefSeq, Jul 2008]
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.019305944).
BP6
Variant 6-109741502-A-T is Benign according to our data. Variant chr6-109741502-A-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 407082.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=7, Likely_benign=5}. Variant chr6-109741502-A-T is described in Lovd as [Likely_benign].
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
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Likely benign, no assertion criteria provided
clinical testing
Clinical Genetics, Academic Medical Center
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Likely benign, criteria provided, single submitter
clinical testing
GeneDx
May 06, 2021
See Variant Classification Assertion Criteria. -
Uncertain significance, criteria provided, single submitter
clinical testing
CeGaT Center for Human Genetics Tuebingen
Dec 01, 2023
FIG4: PM2 -
Uncertain significance, criteria provided, single submitter
clinical testing
Mayo Clinic Laboratories, Mayo Clinic
Oct 07, 2022
BP4 -
Charcot-Marie-Tooth disease type 4J Uncertain:2
Uncertain significance, criteria provided, single submitter
clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Mar 05, 2018
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Uncertain significance, 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 did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Amyotrophic lateral sclerosis type 11 Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter
clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Mar 05, 2018
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Likely 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Uncertain significance, criteria provided, single submitter
clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Mar 05, 2018
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Yunis-Varon syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Mar 05, 2018
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not specified Benign:1
Likely benign, criteria provided, single submitter
clinical testing
Athena Diagnostics
Mar 23, 2021
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Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter
clinical testing
Ambry Genetics
Oct 05, 2021
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
FIG4-related disorder Benign:1
Likely benign, no assertion criteria provided
clinical testing
PreventionGenetics, part of Exact Sciences
May 05, 2022
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Charcot-Marie-Tooth disease type 4 Benign:1
Likely benign, criteria provided, single submitter