chr12-123156306-C-G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.173

Publications

57 publications found
Variant links:
Genes affected
MPHOSPH9 (HGNC:7215): (M-phase phosphoprotein 9) Located in Golgi apparatus and centriole. Implicated in multiple sclerosis. [provided by Alliance of Genome Resources, Apr 2022]

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MPHOSPH9NM_022782.4 linkc.*501G>C 3_prime_UTR_variant Exon 24 of 24 ENST00000606320.6 NP_073619.3 Q99550

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MPHOSPH9ENST00000606320.6 linkc.*501G>C 3_prime_UTR_variant Exon 24 of 24 5 NM_022782.4 ENSP00000475489.1 Q99550
MPHOSPH9ENST00000541603.6 linkc.553-3681G>C intron_variant Intron 5 of 5 1 ENSP00000446362.2 F5H1U6
MPHOSPH9ENST00000541076.6 linkc.*501G>C 3_prime_UTR_variant Exon 22 of 22 5 ENSP00000445859.2 A0A8I5IG87
MPHOSPH9ENST00000545974.5 linkn.*93G>C downstream_gene_variant 4

Frequencies

GnomAD3 genomes
AF:
0.834
AC:
126840
AN:
152098
Hom.:
53197
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.910
Gnomad AMI
AF:
0.828
Gnomad AMR
AF:
0.821
Gnomad ASJ
AF:
0.736
Gnomad EAS
AF:
0.972
Gnomad SAS
AF:
0.741
Gnomad FIN
AF:
0.803
Gnomad MID
AF:
0.723
Gnomad NFE
AF:
0.797
Gnomad OTH
AF:
0.824
GnomAD4 exome
AF:
0.794
AC:
81
AN:
102
Hom.:
31
Cov.:
0
AF XY:
0.729
AC XY:
35
AN XY:
48
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
1.00
AC:
4
AN:
4
Ashkenazi Jewish (ASJ)
AF:
1.00
AC:
2
AN:
2
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.806
AC:
29
AN:
36
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.780
AC:
39
AN:
50
Other (OTH)
AF:
0.700
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:
126947
AN:
152214
Hom.:
53252
Cov.:
33
AF XY:
0.833
AC XY:
61981
AN XY:
74410
show subpopulations
African (AFR)
AF:
0.910
AC:
37824
AN:
41558
American (AMR)
AF:
0.821
AC:
12537
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.736
AC:
2554
AN:
3470
East Asian (EAS)
AF:
0.972
AC:
5045
AN:
5188
South Asian (SAS)
AF:
0.740
AC:
3572
AN:
4824
European-Finnish (FIN)
AF:
0.803
AC:
8494
AN:
10580
Middle Eastern (MID)
AF:
0.723
AC:
211
AN:
292
European-Non Finnish (NFE)
AF:
0.797
AC:
54209
AN:
68002
Other (OTH)
AF:
0.827
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:
0.819
Hom.:
6363
Bravo
AF:
0.839
Asia WGS
AF:
0.871
AC:
3025
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.7
DANN
Benign
0.48
PhyloP100
0.17
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1727313; hg19: chr12-123640853; API