chr2-173091154-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_016653.3(MAP3K20):c.123G>A(p.Glu41=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000347 in 1,613,752 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 0.00018 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
MAP3K20
NM_016653.3 synonymous
NM_016653.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.65
Genes affected
MAP3K20 (HGNC:17797): (mitogen-activated protein kinase kinase kinase 20) This gene is a member of the MAPKKK family of signal transduction molecules and encodes a protein with an N-terminal kinase catalytic domain, followed by a leucine zipper motif and a sterile-alpha motif (SAM). This magnesium-binding protein forms homodimers and is located in the cytoplasm. The protein mediates gamma radiation signaling leading to cell cycle arrest and activity of this protein plays a role in cell cycle checkpoint regulation in cells. The protein also has pro-apoptotic activity. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 2-173091154-G-A is Benign according to our data. Variant chr2-173091154-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1662951.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP3K20 | NM_016653.3 | c.123G>A | p.Glu41= | synonymous_variant | 2/20 | ENST00000375213.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K20 | ENST00000375213.8 | c.123G>A | p.Glu41= | synonymous_variant | 2/20 | 1 | NM_016653.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152050Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000480 AC: 12AN: 250234Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135208
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GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461584Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727064
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GnomAD4 genome AF: 0.000184 AC: 28AN: 152168Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74384
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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 | Invitae | Sep 08, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at