chr19-4117464-G-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_030662.4(MAP2K2):c.258C>A(p.Val86=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000397 in 1,613,874 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 (★★). Synonymous variant affecting the same amino acid position (i.e. V86V) has been classified as Likely benign.
Frequency
Consequence
NM_030662.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2K2 | NM_030662.4 | c.258C>A | p.Val86= | synonymous_variant | 2/11 | ENST00000262948.10 | |
MAP2K2 | XM_006722799.3 | c.258C>A | p.Val86= | synonymous_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K2 | ENST00000262948.10 | c.258C>A | p.Val86= | synonymous_variant | 2/11 | 1 | NM_030662.4 | P1 | |
MAP2K2 | ENST00000394867.9 | n.697C>A | non_coding_transcript_exon_variant | 1/10 | 5 | ||||
MAP2K2 | ENST00000599345.1 | n.455C>A | non_coding_transcript_exon_variant | 2/7 | 5 | ||||
MAP2K2 | ENST00000687128.1 | n.697C>A | non_coding_transcript_exon_variant | 1/7 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000797 AC: 20AN: 250966Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135814
GnomAD4 exome AF: 0.000417 AC: 609AN: 1461676Hom.: 0 Cov.: 36 AF XY: 0.000406 AC XY: 295AN XY: 727138
GnomAD4 genome AF: 0.000210 AC: 32AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74342
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 01, 2008 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 10, 2020 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
RASopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Cardiofaciocutaneous syndrome 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at