16-1706378-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The ENST00000610761.2(MAPK8IP3):c.39G>A(p.Val13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00676 in 1,610,328 control chromosomes in the GnomAD database, including 329 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0043 ( 14 hom., cov: 32)
Exomes 𝑓: 0.0070 ( 315 hom. )
Consequence
MAPK8IP3
ENST00000610761.2 synonymous
ENST00000610761.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.49
Genes affected
MAPK8IP3 (HGNC:6884): (mitogen-activated protein kinase 8 interacting protein 3) The protein encoded by this gene shares similarity with the product of Drosophila syd gene, required for the functional interaction of kinesin I with axonal cargo. Studies of the similar gene in mouse suggested that this protein may interact with, and regulate the activity of numerous protein kinases of the JNK signaling pathway, and thus function as a scaffold protein in neuronal cells. The C. elegans counterpart of this gene is found to regulate synaptic vesicle transport possibly by integrating JNK signaling and kinesin-1 transport. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 16-1706378-G-A is Benign according to our data. Variant chr16-1706378-G-A is described in ClinVar as [Benign]. Clinvar id is 3039422.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1.49 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0726 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAPK8IP3 | NM_001318852.2 | c.39G>A | p.Val13= | synonymous_variant | 1/32 | ENST00000610761.2 | NP_001305781.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPK8IP3 | ENST00000610761.2 | c.39G>A | p.Val13= | synonymous_variant | 1/32 | 1 | NM_001318852.2 | ENSP00000481780 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00430 AC: 654AN: 152194Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.0116 AC: 2800AN: 240906Hom.: 108 AF XY: 0.0153 AC XY: 2006AN XY: 131384
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GnomAD4 exome AF: 0.00701 AC: 10226AN: 1458016Hom.: 315 Cov.: 31 AF XY: 0.00926 AC XY: 6715AN XY: 725102
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GnomAD4 genome AF: 0.00431 AC: 657AN: 152312Hom.: 14 Cov.: 32 AF XY: 0.00567 AC XY: 422AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
MAPK8IP3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 02, 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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at