17-17136247-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAGCAG
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_001364716.4(MPRIP):c.563_568dupGCAGCA(p.Ser188_Ser189dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00021 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
MPRIP
NM_001364716.4 disruptive_inframe_insertion
NM_001364716.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.511
Publications
15 publications found
Genes affected
MPRIP (HGNC:30321): (myosin phosphatase Rho interacting protein) Enables cadherin binding activity. Predicted to be involved in actin filament organization. Located in actin cytoskeleton and cytosol. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001364716.4
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MPRIP | NM_001364716.4 | c.563_568dupGCAGCA | p.Ser188_Ser189dup | disruptive_inframe_insertion | Exon 6 of 24 | ENST00000651222.2 | NP_001351645.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MPRIP | ENST00000651222.2 | c.563_568dupGCAGCA | p.Ser188_Ser189dup | disruptive_inframe_insertion | Exon 6 of 24 | NM_001364716.4 | ENSP00000498253.1 |
Frequencies
GnomAD3 genomes 0.000213 AC: 32AN: 150558Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
32
AN:
150558
Hom.:
Cov.:
0
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: 0.000103 AC: 145AN: 1405352Hom.: 0 Cov.: 0 AF XY: 0.000106 AC XY: 74AN XY: 699204 show subpopulations
GnomAD4 exome
AF:
AC:
145
AN:
1405352
Hom.:
Cov.:
0
AF XY:
AC XY:
74
AN XY:
699204
show subpopulations
African (AFR)
AF:
AC:
20
AN:
32276
American (AMR)
AF:
AC:
0
AN:
42486
Ashkenazi Jewish (ASJ)
AF:
AC:
24
AN:
25202
East Asian (EAS)
AF:
AC:
3
AN:
37396
South Asian (SAS)
AF:
AC:
7
AN:
82924
European-Finnish (FIN)
AF:
AC:
6
AN:
49608
Middle Eastern (MID)
AF:
AC:
0
AN:
5640
European-Non Finnish (NFE)
AF:
AC:
77
AN:
1071916
Other (OTH)
AF:
AC:
8
AN:
57904
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.451
Heterozygous variant carriers
0
9
17
26
34
43
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.000212 AC: 32AN: 150672Hom.: 0 Cov.: 0 AF XY: 0.000258 AC XY: 19AN XY: 73550 show subpopulations
GnomAD4 genome
AF:
AC:
32
AN:
150672
Hom.:
Cov.:
0
AF XY:
AC XY:
19
AN XY:
73550
show subpopulations
African (AFR)
AF:
AC:
19
AN:
40966
American (AMR)
AF:
AC:
2
AN:
15122
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3464
East Asian (EAS)
AF:
AC:
2
AN:
5078
South Asian (SAS)
AF:
AC:
0
AN:
4728
European-Finnish (FIN)
AF:
AC:
0
AN:
10400
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
8
AN:
67626
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
2
4
6
8
10
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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