19-7910353-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_145185.4(MAP2K7):c.427G>A(p.Gly143Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,612,788 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 (★).
Frequency
Consequence
NM_145185.4 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP2K7 | NM_145185.4 | c.427G>A | p.Gly143Ser | missense_variant | 4/11 | ENST00000397979.4 | NP_660186.1 | |
MAP2K7 | NM_001297555.2 | c.475G>A | p.Gly159Ser | missense_variant | 5/12 | NP_001284484.1 | ||
MAP2K7 | NM_001297556.2 | c.427G>A | p.Gly143Ser | missense_variant | 4/11 | NP_001284485.1 | ||
MAP2K7 | XM_006722800.3 | c.475G>A | p.Gly159Ser | missense_variant | 5/12 | XP_006722863.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246302Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134324
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460572Hom.: 0 Cov.: 34 AF XY: 0.0000317 AC XY: 23AN XY: 726560
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.427G>A (p.G143S) alteration is located in exon 4 (coding exon 4) of the MAP2K7 gene. This alteration results from a G to A substitution at nucleotide position 427, causing the glycine (G) at amino acid position 143 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at