22-50603653-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_012324.6(MAPK8IP2):c.475G>C(p.Asp159His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000502 in 1,593,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012324.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPK8IP2 | NM_012324.6 | c.475G>C | p.Asp159His | missense_variant | 4/12 | ENST00000329492.6 | |
MAPK8IP2 | XM_011530679.3 | c.475G>C | p.Asp159His | missense_variant | 4/12 | ||
MAPK8IP2 | XM_011530680.3 | c.475G>C | p.Asp159His | missense_variant | 4/12 | ||
MAPK8IP2 | XM_011530681.3 | c.475G>C | p.Asp159His | missense_variant | 4/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPK8IP2 | ENST00000329492.6 | c.475G>C | p.Asp159His | missense_variant | 4/12 | 1 | NM_012324.6 | P1 | |
MAPK8IP2 | ENST00000008876.7 | n.394G>C | non_coding_transcript_exon_variant | 2/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152204Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1441340Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 715098
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.475G>C (p.D159H) alteration is located in exon 4 (coding exon 4) of the MAPK8IP2 gene. This alteration results from a G to C substitution at nucleotide position 475, causing the aspartic acid (D) at amino acid position 159 to be replaced by a histidine (H). 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