Genetic Variant MPRIP:p.Ser188_Ser189del (chr17-17136247-CCAGCAG-C) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3BA1

The NM_001364716.4(MPRIP):c.563_568delGCAGCA(p.Ser188_Ser189del) variant causes a disruptive inframe deletion 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 0.026 ( 98 hom., cov: 0)

Exomes 𝑓: 0.036 ( 655 hom. )

Failed GnomAD Quality Control

Consequence

MPRIP
NM_001364716.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.67

Publications

15 publications found

Variant links:

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]

MPRIP links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001364716.4

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4 link	c.563_568delGCAGCA	p.Ser188_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 link	c.563_568delGCAGCA	p.Ser188_Ser189del	disruptive_inframe_deletion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1		A0A494BZV2

Frequencies

GnomAD3 genomes

AF:

0.0256

AC:

3854

AN:

150262

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0176

Gnomad AMI

AF:

0.0330

Gnomad AMR

AF:

0.0214

Gnomad ASJ

AF:

0.0277

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.0670

Gnomad FIN

AF:

0.0184

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.0219

Gnomad OTH

AF:

0.0301

GnomAD2 exomes

AF:

0.0311

AC:

6687

AN:

214846

AF XY:

0.0325

show subpopulations

Gnomad AFR exome

AF:

0.0179

Gnomad AMR exome

AF:

0.0162

Gnomad ASJ exome

AF:

0.0174

Gnomad EAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.0163

Gnomad NFE exome

AF:

0.0193

Gnomad OTH exome

AF:

0.0262

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0358

AC:

41041

AN:

1144898

Hom.:

655

AF XY:

0.0376

AC XY:

21274

AN XY:

565974

show subpopulations

African (AFR)

AF:

0.0259

AC:

676

AN:

26146

American (AMR)

AF:

0.0323

AC:

994

AN:

30816

Ashkenazi Jewish (ASJ)

AF:

0.0414

AC:

839

AN:

20266

East Asian (EAS)

AF:

0.194

AC:

4977

AN:

25686

South Asian (SAS)

AF:

0.0953

AC:

5646

AN:

59260

European-Finnish (FIN)

AF:

0.0276

AC:

1007

AN:

36498

Middle Eastern (MID)

AF:

0.0722

AC:

360

AN:

4988

European-Non Finnish (NFE)

AF:

0.0272

AC:

24303

AN:

894438

Other (OTH)

AF:

0.0478

AC:

2239

AN:

46800

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

2136

4272

6407

8543

10679

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0257

AC:

3859

AN:

150370

Hom.:

Cov.:

AF XY:

0.0277

AC XY:

2035

AN XY:

73382

show subpopulations

African (AFR)

AF:

0.0176

AC:

719

AN:

40938

American (AMR)

AF:

0.0214

AC:

323

AN:

15088

Ashkenazi Jewish (ASJ)

AF:

0.0277

AC:

AN:

3460

East Asian (EAS)

AF:

0.124

AC:

629

AN:

5070

South Asian (SAS)

AF:

0.0669

AC:

316

AN:

4726

European-Finnish (FIN)

AF:

0.0184

AC:

190

AN:

10304

Middle Eastern (MID)

AF:

0.0414

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0218

AC:

1475

AN:

67506

Other (OTH)

AF:

0.0332

AC:

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

179

357

536

714

893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0427

Hom.:

3215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.7

Mutation Taster

=193/7

polymorphism (auto)

(source)

Splicing

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

Publications

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17-17136247-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over