17-17136247-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAG

Variant names:

• chr17-17136247-C-CCAG
• rs3833098
• NM_001364716.4:c.566_568dupGCA

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_001364716.4(MPRIP):​c.566_568dupGCA​(p.Ser189dup) variant causes a disruptive inframe insertion 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 0.00060 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00069 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MPRIP NM_001364716.4 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• 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: 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.566_568dupGCA	p.Ser189dup	disruptive_inframe_insertion	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.566_568dupGCA	p.Ser189dup	disruptive_inframe_insertion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.000598 AC: 90 AN: 150554 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000661

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000794

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.000634

Gnomad FIN AF: 0.0000962

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000665

Gnomad OTH AF: 0.000484

GnomAD2 exomes AF: 0.000610 AC: 131 AN: 214846 AF XY: 0.000590

Gnomad AFR exome AF: 0.000677

Gnomad AMR exome AF: 0.000568

Gnomad ASJ exome AF: 0.000224

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000677

Gnomad OTH exome AF: 0.000575

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000695 AC: 976 AN: 1405324 Hom.: 0 Cov.: 0 AF XY: 0.000689 AC XY: 482 AN XY: 699188

African (AFR) AF: 0.000868 AC: 28 AN: 32276

American (AMR) AF: 0.000518 AC: 22 AN: 42486

Ashkenazi Jewish (ASJ) AF: 0.000119 AC: 3 AN: 25202

East Asian (EAS) AF: 0.000160 AC: 6 AN: 37396

South Asian (SAS) AF: 0.00112 AC: 93 AN: 82922

European-Finnish (FIN) AF: 0.0000202 AC: 1 AN: 49608

Middle Eastern (MID) AF: 0.000887 AC: 5 AN: 5640

European-Non Finnish (NFE) AF: 0.000723 AC: 775 AN: 1071892

Other (OTH) AF: 0.000743 AC: 43 AN: 57902

GnomAD4 genome AF: 0.000604 AC: 91 AN: 150668 Hom.: 0 Cov.: 0 AF XY: 0.000693 AC XY: 51 AN XY: 73548

African (AFR) AF: 0.000659 AC: 27 AN: 40962

American (AMR) AF: 0.000794 AC: 12 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.000394 AC: 2 AN: 5078

South Asian (SAS) AF: 0.000635 AC: 3 AN: 4728

European-Finnish (FIN) AF: 0.0000962 AC: 1 AN: 10400

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000665 AC: 45 AN: 67626

Other (OTH) AF: 0.000479 AC: 1 AN: 2088

Alfa AF: 0.000763 Hom.: 3215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.51
Mutation Taster		=76/24	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3833098; hg19: chr17-17039561;