chr11-63902743-C-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001039469.3(MARK2):c.1377C>A(p.Pro459=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00182 in 1,613,662 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 25 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 19 hom. )
Consequence
MARK2
NM_001039469.3 synonymous
NM_001039469.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.15
Genes affected
MARK2 (HGNC:3332): (microtubule affinity regulating kinase 2) This gene encodes a member of the Par-1 family of serine/threonine protein kinases. The protein is an important regulator of cell polarity in epithelial and neuronal cells, and also controls the stability of microtubules through phosphorylation and inactivation of several microtubule-associating proteins. The protein localizes to cell membranes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
Variant 11-63902743-C-A is Benign according to our data. Variant chr11-63902743-C-A is described in ClinVar as [Benign]. Clinvar id is 711552.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.15 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00892 (1359/152274) while in subpopulation AFR AF= 0.0295 (1225/41544). AF 95% confidence interval is 0.0281. There are 25 homozygotes in gnomad4. There are 640 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1356 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MARK2 | NM_001039469.3 | c.1377C>A | p.Pro459= | synonymous_variant | 13/19 | ENST00000402010.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MARK2 | ENST00000402010.8 | c.1377C>A | p.Pro459= | synonymous_variant | 13/19 | 1 | NM_001039469.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00891 AC: 1356AN: 152156Hom.: 25 Cov.: 32
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GnomAD3 exomes AF: 0.00248 AC: 621AN: 250856Hom.: 9 AF XY: 0.00191 AC XY: 259AN XY: 135650
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GnomAD4 exome AF: 0.00108 AC: 1574AN: 1461388Hom.: 19 Cov.: 32 AF XY: 0.000988 AC XY: 718AN XY: 727020
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GnomAD4 genome ? AF: 0.00892 AC: 1359AN: 152274Hom.: 25 Cov.: 32 AF XY: 0.00860 AC XY: 640AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
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