chr12-123194395-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022782.4(MPHOSPH9):c.2232G>A(p.Met744Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000558 in 1,433,910 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000056 ( 0 hom. )
Consequence
MPHOSPH9
NM_022782.4 missense
NM_022782.4 missense
Scores
1
9
6
Clinical Significance
Conservation
PhyloP100: 4.68
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPHOSPH9 | NM_022782.4 | c.2232G>A | p.Met744Ile | missense_variant | 13/24 | ENST00000606320.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPHOSPH9 | ENST00000606320.6 | c.2232G>A | p.Met744Ile | missense_variant | 13/24 | 5 | NM_022782.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000440 AC: 1AN: 227332Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122474
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GnomAD4 exome AF: 0.00000558 AC: 8AN: 1433910Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 711936
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1776G>A (p.M592I) alteration is located in exon 9 (coding exon 9) of the MPHOSPH9 gene. This alteration results from a G to A substitution at nucleotide position 1776, causing the methionine (M) at amino acid position 592 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
REVEL
Uncertain
Sift4G
Benign
T;T
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at