chr14-103475117-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001128918.3(MARK3):c.1389G>A(p.Lys463=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,614,090 control chromosomes in the GnomAD database, including 167 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 28 hom., cov: 33)
Exomes 𝑓: 0.013 ( 139 hom. )
Consequence
MARK3
NM_001128918.3 synonymous
NM_001128918.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.54
Genes affected
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 14-103475117-G-A is Benign according to our data. Variant chr14-103475117-G-A is described in ClinVar as [Benign]. Clinvar id is 3044255.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.54 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 28 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MARK3 | NM_001128918.3 | c.1389G>A | p.Lys463= | synonymous_variant | 13/18 | ENST00000429436.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MARK3 | ENST00000429436.7 | c.1389G>A | p.Lys463= | synonymous_variant | 13/18 | 1 | NM_001128918.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0106 AC: 1612AN: 152222Hom.: 28 Cov.: 33
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GnomAD3 exomes AF: 0.0115 AC: 2871AN: 249524Hom.: 30 AF XY: 0.0112 AC XY: 1518AN XY: 135382
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GnomAD4 exome AF: 0.0126 AC: 18480AN: 1461750Hom.: 139 Cov.: 31 AF XY: 0.0124 AC XY: 9038AN XY: 727180
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MARK3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 2019 | 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). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at