Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001128918.3(MARK3):c.413-4A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,572,776 control chromosomes in the GnomAD database, including 91,062 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
MARK3 (HGNC:6897): (microtubule affinity regulating kinase 3) The protein encoded by this gene is activated by phosphorylation and in turn is involved in the phosphorylation of tau proteins MAP2 and MAP4. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 14-103457138-A-G is Benign according to our data. Variant chr14-103457138-A-G is described in ClinVar as [Benign]. Clinvar id is 1321158.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.
Review Status: criteria provided, single submitter
Collection Method: not provided
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MARK3-related disorder Benign:1
Oct 22, 2019
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Visual impairment and progressive phthisis bulbi Benign:1
Sep 05, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter