18-50664007-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002747.4(MAPK4):c.49G>A(p.Gly17Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,613,590 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G17D) has been classified as Uncertain significance.
Frequency
Consequence
NM_002747.4 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 | UniProt |
---|---|---|---|---|---|---|---|
MAPK4 | NM_002747.4 | c.49G>A | p.Gly17Ser | missense_variant | 2/6 | ENST00000400384.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK4 | ENST00000400384.7 | c.49G>A | p.Gly17Ser | missense_variant | 2/6 | 1 | NM_002747.4 | P1 | |
MAPK4 | ENST00000588540.1 | c.49G>A | p.Gly17Ser | missense_variant | 2/3 | 1 | |||
MAPK4 | ENST00000592595.5 | c.49G>A | p.Gly17Ser | missense_variant | 2/4 | 1 | |||
MAPK4 | ENST00000540640.3 | c.-87-51072G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000562 AC: 14AN: 249138Hom.: 0 AF XY: 0.0000814 AC XY: 11AN XY: 135194
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1461414Hom.: 1 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 726994
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.49G>A (p.G17S) alteration is located in exon 2 (coding exon 1) of the MAPK4 gene. This alteration results from a G to A substitution at nucleotide position 49, causing the glycine (G) at amino acid position 17 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