17-17136247-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAG

Variant names:

• chr17-17136247-CCAG-C
• rs3833098
• NM_001364716.4:c.566_568delGCA

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3 BA1

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
• 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]

ACMG classification

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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPRIP	NM_001364716.4	MANE Select	c.566_568delGCA	p.Ser189del	disruptive_inframe_deletion	Exon 6 of 24	NP_001351645.2	A0A494BZV2
	MPRIP	NM_015134.4		c.566_568delGCA	p.Ser189del	disruptive_inframe_deletion	Exon 6 of 23	NP_055949.2	Q6WCQ1-2
	MPRIP	NM_201274.4		c.566_568delGCA	p.Ser189del	disruptive_inframe_deletion	Exon 6 of 24	NP_958431.2	Q6WCQ1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPRIP	ENST00000651222.2	MANE Select	c.566_568delGCA	p.Ser189del	disruptive_inframe_deletion	Exon 6 of 24	ENSP00000498253.1	A0A494BZV2
	MPRIP	ENST00000395811.9	TSL:1	c.566_568delGCA	p.Ser189del	disruptive_inframe_deletion	Exon 6 of 23	ENSP00000379156.4	Q6WCQ1-2
	MPRIP	ENST00000584067.5	TSL:1	c.98_100delGCA	p.Ser33del	disruptive_inframe_deletion	Exon 2 of 18	ENSP00000462688.1	J3KSW8

Frequencies

GnomAD3 genomes AF: 0.720 AC: 108275 AN: 150448 Hom.: 39042 Cov.: 0

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

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

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

GnomAD4 genome AF: 0.720 AC: 108367 AN: 150562 Hom.: 39080 Cov.: 0 AF XY: 0.725 AC XY: 53298 AN XY: 73488

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

Alfa AF: 0.660 Hom.: 3215

Bravo AF: 0.739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.7
Mutation Taster		=65/35	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3833098; hg19: chr17-17039561; COSMIC: COSV59044465; COSMIC: COSV59044465;