12-123181203-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022782.4(MPHOSPH9):c.2249G>A(p.Gly750Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,611,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022782.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPHOSPH9 | NM_022782.4 | c.2249G>A | p.Gly750Glu | missense_variant | 14/24 | ENST00000606320.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPHOSPH9 | ENST00000606320.6 | c.2249G>A | p.Gly750Glu | missense_variant | 14/24 | 5 | NM_022782.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151978Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459622Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726274
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151978Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.1793G>A (p.G598E) alteration is located in exon 10 (coding exon 10) of the MPHOSPH9 gene. This alteration results from a G to A substitution at nucleotide position 1793, causing the glycine (G) at amino acid position 598 to be replaced by a glutamic acid (E). 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