chr17-17136247-CCAGCAG-C

Variant names:

• chr17-17136247-CCAGCAG-C
• rs3833098
• NM_001364716.4:c.563_568delGCAGCA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4	c.563_568delGCAGCA	p.Ser188_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	c.563_568delGCAGCA	p.Ser188_Ser189del	disruptive_inframe_deletion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.0256 AC: 3854 AN: 150262 Hom.: 96 Cov.: 0

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

GnomAD3 exomes AF: 0.0311 AC: 6687 AN: 214846 Hom.: 179 AF XY: 0.0325 AC XY: 3798 AN XY: 116878

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 SAS exome AF: 0.0539

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

Gnomad4 AFR exome AF: 0.0259

Gnomad4 AMR exome AF: 0.0323

Gnomad4 ASJ exome AF: 0.0414

Gnomad4 EAS exome AF: 0.194

Gnomad4 SAS exome AF: 0.0953

Gnomad4 FIN exome AF: 0.0276

Gnomad4 NFE exome AF: 0.0272

Gnomad4 OTH exome AF: 0.0478

GnomAD4 genome AF: 0.0257 AC: 3859 AN: 150370 Hom.: 98 Cov.: 0 AF XY: 0.0277 AC XY: 2035 AN XY: 73382

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0669

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0332

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;