chr16-30118056-C-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_002746.3(MAPK3):c.651G>T(p.Leu217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000305 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00031 ( 0 hom. )
Consequence
MAPK3
NM_002746.3 synonymous
NM_002746.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.429
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 -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 16-30118056-C-A is Benign according to our data. Variant chr16-30118056-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2646380.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.429 with no splicing effect.
BS2
High AC in GnomAd4 at 40 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPK3 | NM_002746.3 | c.651G>T | p.Leu217= | synonymous_variant | 4/9 | ENST00000263025.9 | |
MAPK3 | NM_001040056.3 | c.651G>T | p.Leu217= | synonymous_variant | 4/7 | ||
MAPK3 | NM_001109891.2 | c.651G>T | p.Leu217= | synonymous_variant | 4/8 | ||
MAPK3 | XR_243293.2 | n.662G>T | non_coding_transcript_exon_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK3 | ENST00000263025.9 | c.651G>T | p.Leu217= | synonymous_variant | 4/9 | 1 | NM_002746.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152200Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000462 AC: 116AN: 250966Hom.: 0 AF XY: 0.000471 AC XY: 64AN XY: 135738
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GnomAD4 exome AF: 0.000310 AC: 453AN: 1461688Hom.: 0 Cov.: 31 AF XY: 0.000304 AC XY: 221AN XY: 727152
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GnomAD4 genome AF: 0.000263 AC: 40AN: 152316Hom.: 0 Cov.: 31 AF XY: 0.000242 AC XY: 18AN XY: 74474
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | MAPK3: BP4, BP7 - |
Computational scores
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CADD
Benign
DANN
Benign
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