19-4099286-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_030662.4(MAP2K2):c.834C>A(p.Ile278Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,454,860 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
Consequence
NM_030662.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP2K2 | NM_030662.4 | c.834C>A | p.Ile278Ile | synonymous_variant | Exon 7 of 11 | ENST00000262948.10 | NP_109587.1 | |
MAP2K2 | XM_047439100.1 | c.264C>A | p.Ile88Ile | synonymous_variant | Exon 5 of 9 | XP_047295056.1 | ||
MAP2K2 | XM_006722799.3 | c.705+1733C>A | intron_variant | Intron 6 of 8 | XP_006722862.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000425 AC: 1AN: 235228Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128164
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1454860Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 723278
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
p.Ile278Ile in exon 7 of MAP2K2: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 1/7050 Latino ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs766540227). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at