chr17-17136247-CCAGCAGCAGCAGCAGCAG-C
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_001364716.4(MPRIP):c.551_568delGCAGCAGCAGCAGCAGCA(p.Ser184_Ser189del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000662 in 1,555,910 control chromosomes in the GnomAD database, including 1 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00052 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00068 ( 1 hom. )
Consequence
MPRIP
NM_001364716.4 disruptive_inframe_deletion
NM_001364716.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.67
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.551_568delGCAGCAGCAGCAGCAGCA | p.Ser184_Ser189del | disruptive_inframe_deletion | 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.551_568delGCAGCAGCAGCAGCAGCA | p.Ser184_Ser189del | disruptive_inframe_deletion | Exon 6 of 24 | NM_001364716.4 | ENSP00000498253.1 |
Frequencies
GnomAD3 genomes 0.000525 AC: 79AN: 150558Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
79
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:
GnomAD2 exomes AF: 0.000666 AC: 143AN: 214846 AF XY: 0.000659 show subpopulations
GnomAD2 exomes
AF:
AC:
143
AN:
214846
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000677 AC: 951AN: 1405238Hom.: 1 AF XY: 0.000644 AC XY: 450AN XY: 699134 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
951
AN:
1405238
Hom.:
AF XY:
AC XY:
450
AN XY:
699134
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
13
AN:
32274
American (AMR)
AF:
AC:
4
AN:
42486
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
25202
East Asian (EAS)
AF:
AC:
6
AN:
37396
South Asian (SAS)
AF:
AC:
17
AN:
82924
European-Finnish (FIN)
AF:
AC:
7
AN:
49608
Middle Eastern (MID)
AF:
AC:
0
AN:
5640
European-Non Finnish (NFE)
AF:
AC:
888
AN:
1071808
Other (OTH)
AF:
AC:
15
AN:
57900
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.381
Heterozygous variant carriers
0
37
73
110
146
183
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.000524 AC: 79AN: 150672Hom.: 0 Cov.: 0 AF XY: 0.000476 AC XY: 35AN XY: 73550 show subpopulations
GnomAD4 genome
AF:
AC:
79
AN:
150672
Hom.:
Cov.:
0
AF XY:
AC XY:
35
AN XY:
73550
show subpopulations
African (AFR)
AF:
AC:
15
AN:
40966
American (AMR)
AF:
AC:
2
AN:
15122
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5078
South Asian (SAS)
AF:
AC:
2
AN:
4728
European-Finnish (FIN)
AF:
AC:
0
AN:
10400
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
59
AN:
67626
Other (OTH)
AF:
AC:
1
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.516
Heterozygous variant carriers
0
4
7
11
14
18
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
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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