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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364716.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MPRIP	NM_001364716.4	MANE Select	c.563_568delGCAGCA	p.Ser188_Ser189del	disruptive_inframe_deletion	Exon 6 of 24	NP_001351645.2	A0A494BZV2
MPRIP	NM_015134.4		c.563_568delGCAGCA	p.Ser188_Ser189del	disruptive_inframe_deletion	Exon 6 of 23	NP_055949.2	Q6WCQ1-2
MPRIP	NM_201274.4		c.563_568delGCAGCA	p.Ser188_Ser189del	disruptive_inframe_deletion	Exon 6 of 24	NP_958431.2	Q6WCQ1-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MPRIP	ENST00000651222.2	MANE Select	c.563_568delGCAGCA	p.Ser188_Ser189del	disruptive_inframe_deletion	Exon 6 of 24	ENSP00000498253.1	A0A494BZV2
MPRIP	ENST00000395811.9	TSL:1	c.563_568delGCAGCA	p.Ser188_Ser189del	disruptive_inframe_deletion	Exon 6 of 23	ENSP00000379156.4	Q6WCQ1-2
MPRIP	ENST00000584067.5	TSL:1	c.95_100delGCAGCA	p.Ser32_Ser33del	disruptive_inframe_deletion	Exon 2 of 18	ENSP00000462688.1	J3KSW8

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

Age Distribution

Exome Het

Exome Hom

Variant carriers

1048

2096

3144

4192

5240

<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:

0.0257

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

168

224

280

<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:

0.0427

Hom.:

3215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over