17-17136247-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAGCAGCAGCAGCAG

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

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

Verdict is Likely_benign. Variant got -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

GnomAD3 exomes AF: 0.000610 AC: 131 AN: 214846 Hom.: 0 AF XY: 0.000590 AC XY: 69 AN XY: 116878

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 SAS exome AF: 0.00127

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

Gnomad4 AFR exome AF: 0.000868

Gnomad4 AMR exome AF: 0.000518

Gnomad4 ASJ exome AF: 0.000119

Gnomad4 EAS exome AF: 0.000160

Gnomad4 SAS exome AF: 0.00112

Gnomad4 FIN exome AF: 0.0000202

Gnomad4 NFE exome AF: 0.000723

Gnomad4 OTH exome AF: 0.000743

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

Gnomad4 AFR AF: 0.000659

Gnomad4 AMR AF: 0.000794

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000394

Gnomad4 SAS AF: 0.000635

Gnomad4 FIN AF: 0.0000962

Gnomad4 NFE AF: 0.000665

Gnomad4 OTH AF: 0.000479

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3833098; hg19: chr17-17039561;