chr19-4123844-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030662.4(MAP2K2):āc.32C>Gā(p.Ala11Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000726 in 1,377,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. A11A) has been classified as Likely benign.
Frequency
Consequence
NM_030662.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2K2 | NM_030662.4 | c.32C>G | p.Ala11Gly | missense_variant | 1/11 | ENST00000262948.10 | |
MAP2K2 | XM_006722799.3 | c.32C>G | p.Ala11Gly | missense_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K2 | ENST00000262948.10 | c.32C>G | p.Ala11Gly | missense_variant | 1/11 | 1 | NM_030662.4 | P1 | |
MAP2K2 | ENST00000599345.1 | n.229C>G | non_coding_transcript_exon_variant | 1/7 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 7.26e-7 AC: 1AN: 1377298Hom.: 0 Cov.: 31 AF XY: 0.00000147 AC XY: 1AN XY: 681360
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 01, 2018 | Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: in Gnomad 19:4123841 G / C-not present, but coverage not ideal; not in ClinVar, HGMD, or Google search; predicted benign, gene not in many animals, but well-conserved in those - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at