Genetic Variant NM_001364716.4:c.566_568delGCA (chr17-17136247-CCAG-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.566_568delGCA(p.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 0.72 ( 39080 hom., cov: 0)

Exomes 𝑓: 0.61 ( 210261 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 = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4 link	c.566_568delGCA	p.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.566_568delGCA	p.Ser189del	disruptive_inframe_deletion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1		A0A494BZV2

Frequencies

GnomAD3 genomes

AF:

0.720

AC:

108275

AN:

150448

Hom.:

39042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.703

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.737

Gnomad ASJ

AF:

0.687

Gnomad EAS

AF:

0.861

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.818

Gnomad MID

AF:

0.596

Gnomad NFE

AF:

0.699

Gnomad OTH

AF:

0.695

GnomAD2 exomes

AF:

0.717

AC:

153947

AN:

214846

AF XY:

0.718

show subpopulations

Gnomad AFR exome

AF:

0.653

Gnomad AMR exome

AF:

0.769

Gnomad ASJ exome

AF:

0.680

Gnomad EAS exome

AF:

0.838

Gnomad FIN exome

AF:

0.796

Gnomad NFE exome

AF:

0.672

Gnomad OTH exome

AF:

0.684

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.611

AC:

849553

AN:

1389348

Hom.:

210261

AF XY:

0.611

AC XY:

422077

AN XY:

691266

show subpopulations

African (AFR)

AF:

0.597

AC:

19034

AN:

31874

American (AMR)

AF:

0.631

AC:

26523

AN:

42066

Ashkenazi Jewish (ASJ)

AF:

0.575

AC:

14214

AN:

24730

East Asian (EAS)

AF:

0.684

AC:

25575

AN:

37372

South Asian (SAS)

AF:

0.602

AC:

49315

AN:

81972

European-Finnish (FIN)

AF:

0.656

AC:

32343

AN:

49290

Middle Eastern (MID)

AF:

0.551

AC:

3062

AN:

5560

European-Non Finnish (NFE)

AF:

0.609

AC:

645093

AN:

1059340

Other (OTH)

AF:

0.602

AC:

34394

AN:

57144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.603

Heterozygous variant carriers

18214

36428

54642

72856

91070

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.720

AC:

108367

AN:

150562

Hom.:

39080

Cov.:

AF XY:

0.725

AC XY:

53298

AN XY:

73488

show subpopulations

African (AFR)

AF:

0.703

AC:

28780

AN:

40936

American (AMR)

AF:

0.737

AC:

11139

AN:

15110

Ashkenazi Jewish (ASJ)

AF:

0.687

AC:

2379

AN:

3462

East Asian (EAS)

AF:

0.860

AC:

4364

AN:

5072

South Asian (SAS)

AF:

0.759

AC:

3586

AN:

4724

European-Finnish (FIN)

AF:

0.818

AC:

8506

AN:

10394

Middle Eastern (MID)

AF:

0.592

AC:

173

AN:

292

European-Non Finnish (NFE)

AF:

0.699

AC:

47229

AN:

67584

Other (OTH)

AF:

0.694

AC:

1444

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1458

2916

4374

5832

7290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.660

Hom.:

3215

Bravo

AF:

0.739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.7

Mutation Taster

=65/35

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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NM_001364716.4:c.566_568delGCA

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