rs16949924
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002755.4(MAP2K1):c.291+22G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,596,254 control chromosomes in the GnomAD database, including 91,229 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.28 ( 6512 hom., cov: 31)
Exomes 𝑓: 0.34 ( 84717 hom. )
Consequence
MAP2K1
NM_002755.4 intron
NM_002755.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.115
Genes affected
MAP2K1 (HGNC:6840): (mitogen-activated protein kinase kinase 1) The protein encoded by this gene is a member of the dual specificity protein kinase family, which acts as a mitogen-activated protein (MAP) kinase kinase. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act as an integration point for multiple biochemical signals. This protein kinase lies upstream of MAP kinases and stimulates the enzymatic activity of MAP kinases upon wide variety of extra- and intracellular signals. As an essential component of MAP kinase signal transduction pathway, this kinase is involved in many cellular processes such as proliferation, differentiation, transcription regulation and development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 15-66435259-G-C is Benign according to our data. Variant chr15-66435259-G-C is described in ClinVar as [Benign]. Clinvar id is 40784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2K1 | NM_002755.4 | c.291+22G>C | intron_variant | ENST00000307102.10 | |||
MAP2K1 | NM_001411065.1 | c.225+22G>C | intron_variant | ||||
MAP2K1 | XM_011521783.4 | c.225+22G>C | intron_variant | ||||
MAP2K1 | XM_017022411.3 | c.291+22G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K1 | ENST00000307102.10 | c.291+22G>C | intron_variant | 1 | NM_002755.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.277 AC: 42103AN: 151780Hom.: 6506 Cov.: 31
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GnomAD3 exomes AF: 0.319 AC: 80030AN: 250750Hom.: 13235 AF XY: 0.324 AC XY: 43972AN XY: 135584
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GnomAD4 exome AF: 0.338 AC: 488843AN: 1444356Hom.: 84717 Cov.: 28 AF XY: 0.339 AC XY: 243956AN XY: 719736
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GnomAD4 genome ? AF: 0.277 AC: 42130AN: 151898Hom.: 6512 Cov.: 31 AF XY: 0.278 AC XY: 20657AN XY: 74222
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Squamous cell lung carcinoma Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing;in vivo | Faculté Pluridciplinaire Nador, Université Mohamed Premier | May 05, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Cardiofaciocutaneous syndrome 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
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