chr19-4090579-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_030662.4(MAP2K2):c.*19C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00207 in 1,540,100 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_030662.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP2K2 | NM_030662.4 | c.*19C>T | 3_prime_UTR_variant | Exon 11 of 11 | ENST00000262948.10 | NP_109587.1 | ||
MAP2K2 | XM_006722799.3 | c.*19C>T | 3_prime_UTR_variant | Exon 9 of 9 | XP_006722862.1 | |||
MAP2K2 | XM_047439100.1 | c.*19C>T | 3_prime_UTR_variant | Exon 9 of 9 | XP_047295056.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00141 AC: 215AN: 152210Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00164 AC: 252AN: 153956Hom.: 0 AF XY: 0.00166 AC XY: 135AN XY: 81520
GnomAD4 exome AF: 0.00215 AC: 2981AN: 1387772Hom.: 4 Cov.: 30 AF XY: 0.00217 AC XY: 1490AN XY: 685132
GnomAD4 genome AF: 0.00140 AC: 214AN: 152328Hom.: 1 Cov.: 33 AF XY: 0.00125 AC XY: 93AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Variant summary: MAP2K2 c.*19C>T is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.0016 in 153956 control chromosomes (gnomAD). The observed variant frequency is approximately 655 fold of the estimated maximal expected allele frequency for a pathogenic variant in MAP2K2 causing Noonan Syndrome and Related Conditions phenotype (2.5e-06), strongly suggesting that the variant is benign. To our knowledge, no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign. -
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at