chr16-1706378-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001318852.2(MAPK8IP3):c.39G>A(p.Val13Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00676 in 1,610,328 control chromosomes in the GnomAD database, including 329 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001318852.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAPK8IP3 | NM_001318852.2 | c.39G>A | p.Val13Val | 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.39G>A | p.Val13Val | synonymous_variant | Exon 1 of 32 | 1 | NM_001318852.2 | ENSP00000481780.1 |
Frequencies
GnomAD3 genomes AF: 0.00430 AC: 654AN: 152194Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.0116 AC: 2800AN: 240906Hom.: 108 AF XY: 0.0153 AC XY: 2006AN XY: 131384
GnomAD4 exome AF: 0.00701 AC: 10226AN: 1458016Hom.: 315 Cov.: 31 AF XY: 0.00926 AC XY: 6715AN XY: 725102
GnomAD4 genome AF: 0.00431 AC: 657AN: 152312Hom.: 14 Cov.: 32 AF XY: 0.00567 AC XY: 422AN XY: 74486
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at