chr12-123156306-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022782.4(MPHOSPH9):c.*501G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,316 control chromosomes in the GnomAD database, including 53,283 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.83 ( 53252 hom., cov: 33)
Exomes 𝑓: 0.79 ( 31 hom. )
Consequence
MPHOSPH9
NM_022782.4 3_prime_UTR
NM_022782.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.173
Publications
57 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPHOSPH9 | ENST00000606320.6 | c.*501G>C | 3_prime_UTR_variant | Exon 24 of 24 | 5 | NM_022782.4 | ENSP00000475489.1 | |||
MPHOSPH9 | ENST00000541603.6 | c.553-3681G>C | intron_variant | Intron 5 of 5 | 1 | ENSP00000446362.2 | ||||
MPHOSPH9 | ENST00000541076.6 | c.*501G>C | 3_prime_UTR_variant | Exon 22 of 22 | 5 | ENSP00000445859.2 | ||||
MPHOSPH9 | ENST00000545974.5 | n.*93G>C | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.834 AC: 126840AN: 152098Hom.: 53197 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
126840
AN:
152098
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.794 AC: 81AN: 102Hom.: 31 Cov.: 0 AF XY: 0.729 AC XY: 35AN XY: 48 show subpopulations
GnomAD4 exome
AF:
AC:
81
AN:
102
Hom.:
Cov.:
0
AF XY:
AC XY:
35
AN XY:
48
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
4
AN:
4
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
2
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
29
AN:
36
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
39
AN:
50
Other (OTH)
AF:
AC:
7
AN:
10
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.541
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.834 AC: 126947AN: 152214Hom.: 53252 Cov.: 33 AF XY: 0.833 AC XY: 61981AN XY: 74410 show subpopulations
GnomAD4 genome
AF:
AC:
126947
AN:
152214
Hom.:
Cov.:
33
AF XY:
AC XY:
61981
AN XY:
74410
show subpopulations
African (AFR)
AF:
AC:
37824
AN:
41558
American (AMR)
AF:
AC:
12537
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
2554
AN:
3470
East Asian (EAS)
AF:
AC:
5045
AN:
5188
South Asian (SAS)
AF:
AC:
3572
AN:
4824
European-Finnish (FIN)
AF:
AC:
8494
AN:
10580
Middle Eastern (MID)
AF:
AC:
211
AN:
292
European-Non Finnish (NFE)
AF:
AC:
54209
AN:
68002
Other (OTH)
AF:
AC:
1746
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1077
2154
3230
4307
5384
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
886
1772
2658
3544
4430
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3025
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.