chr16-30116846-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The ENST00000395199.7(MAPK3):c.1065G>A(p.Gly355=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000924 in 1,613,164 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0050 ( 7 hom., cov: 31)
Exomes 𝑓: 0.00050 ( 10 hom. )
Consequence
MAPK3
ENST00000395199.7 synonymous
ENST00000395199.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0760
Genes affected
MAPK3 (HGNC:6877): (mitogen-activated protein kinase 3) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act in a signaling cascade that regulates various cellular processes such as proliferation, differentiation, and cell cycle progression in response to a variety of extracellular signals. This kinase is activated by upstream kinases, resulting in its translocation to the nucleus where it phosphorylates nuclear targets. Alternatively spliced transcript variants encoding different protein isoforms have been described. [provided by RefSeq, Jul 2008]
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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=-0.84).
BP6
?
Variant 16-30116846-C-T is Benign according to our data. Variant chr16-30116846-C-T is described in ClinVar as [Benign]. Clinvar id is 3056883.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.076 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00497 (757/152224) while in subpopulation AFR AF= 0.0172 (714/41516). AF 95% confidence interval is 0.0162. There are 7 homozygotes in gnomad4. There are 377 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 757 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPK3 | NM_002746.3 | c.1017+48G>A | intron_variant | ENST00000263025.9 | |||
MAPK3 | NM_001040056.3 | c.1065G>A | p.Gly355= | synonymous_variant | 7/7 | ||
MAPK3 | NM_001109891.2 | c.885+48G>A | intron_variant | ||||
MAPK3 | XR_243293.2 | n.1028+48G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK3 | ENST00000263025.9 | c.1017+48G>A | intron_variant | 1 | NM_002746.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00498 AC: 757AN: 152106Hom.: 7 Cov.: 31
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GnomAD3 exomes AF: 0.00131 AC: 322AN: 246546Hom.: 3 AF XY: 0.000864 AC XY: 116AN XY: 134280
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GnomAD4 exome AF: 0.000502 AC: 733AN: 1460940Hom.: 10 Cov.: 32 AF XY: 0.000422 AC XY: 307AN XY: 726758
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MAPK3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 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
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