17-17136247-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAG

Variant names:

• chr17-17136247-CCAGCAGCAGCAG-C
• rs3833098
• NM_001364716.4:c.557_568delGCAGCAGCAGCA

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3 BS2

The NM_001364716.4(MPRIP):​c.557_568delGCAGCAGCAGCA​(p.Ser186_Ser189del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,555,896 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0030 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0015 (3 hom.)
• 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 Likely_benign. Variant got -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001364716.4
• BS2: High Homozygotes in GnomAdExome4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4	c.557_568delGCAGCAGCAGCA	p.Ser186_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.557_568delGCAGCAGCAGCA	p.Ser186_Ser189del	disruptive_inframe_deletion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.00306 AC: 460 AN: 150558 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00649

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00212

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000393

Gnomad SAS AF: 0.000211

Gnomad FIN AF: 0.00250

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00185

Gnomad OTH AF: 0.00339

GnomAD3 exomes AF: 0.00152 AC: 326 AN: 214846 Hom.: 1 AF XY: 0.00140 AC XY: 164 AN XY: 116878

Gnomad AFR exome AF: 0.00699

Gnomad AMR exome AF: 0.000702

Gnomad ASJ exome AF: 0.000224

Gnomad EAS exome AF: 0.000642

Gnomad SAS exome AF: 0.000112

Gnomad FIN exome AF: 0.00238

Gnomad NFE exome AF: 0.00148

Gnomad OTH exome AF: 0.00153

GnomAD4 exome AF: 0.00149 AC: 2096 AN: 1405224 Hom.: 3 AF XY: 0.00150 AC XY: 1051 AN XY: 699132

Gnomad4 AFR exome AF: 0.00822

Gnomad4 AMR exome AF: 0.00101

Gnomad4 ASJ exome AF: 0.000119

Gnomad4 EAS exome AF: 0.000374

Gnomad4 SAS exome AF: 0.000181

Gnomad4 FIN exome AF: 0.00325

Gnomad4 NFE exome AF: 0.00140

Gnomad4 OTH exome AF: 0.00157

GnomAD4 genome AF: 0.00304 AC: 458 AN: 150672 Hom.: 1 Cov.: 0 AF XY: 0.00325 AC XY: 239 AN XY: 73550

Gnomad4 AFR AF: 0.00640

Gnomad4 AMR AF: 0.00212

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000394

Gnomad4 SAS AF: 0.000212

Gnomad4 FIN AF: 0.00250

Gnomad4 NFE AF: 0.00185

Gnomad4 OTH AF: 0.00383

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;