16-1706348-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001318852.2(MAPK8IP3):c.9G>A(p.Glu3Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00699 in 1,586,738 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001318852.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAPK8IP3 | NM_001318852.2 | c.9G>A | p.Glu3Glu | synonymous_variant | Exon 1 of 32 | ENST00000610761.2 | NP_001305781.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPK8IP3 | ENST00000610761.2 | c.9G>A | p.Glu3Glu | synonymous_variant | Exon 1 of 32 | 1 | NM_001318852.2 | ENSP00000481780.1 |
Frequencies
GnomAD3 genomes AF: 0.00481 AC: 732AN: 152180Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00566 AC: 1163AN: 205598Hom.: 5 AF XY: 0.00545 AC XY: 614AN XY: 112654
GnomAD4 exome AF: 0.00723 AC: 10367AN: 1434442Hom.: 60 Cov.: 31 AF XY: 0.00697 AC XY: 4961AN XY: 711324
GnomAD4 genome AF: 0.00480 AC: 731AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.00426 AC XY: 317AN XY: 74474
ClinVar
Submissions by phenotype
MAPK8IP3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
MAPK8IP3: BP4, BP7, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at