17-17136247-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAG

Variant names:

• chr17-17136247-CCAGCAGCAGCAGCAG-C
• rs3833098
• NM_001364716.4:c.554_568delGCAGCAGCAGCAGCA

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP3

The NM_001364716.4(MPRIP):​c.554_568delGCAGCAGCAGCAGCA​(p.Ser185_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 0.000114 in 1,556,024 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00011 (1 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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• 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.554_568delGCAGCAGCAGCAGCA	p.Ser185_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.554_568delGCAGCAGCAGCAGCA	p.Ser185_Ser189del	disruptive_inframe_deletion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.000133 AC: 20 AN: 150558 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000393

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000112 AC: 157 AN: 1405352 Hom.: 1 AF XY: 0.000119 AC XY: 83 AN XY: 699200

Gnomad4 AFR exome AF: 0.000124

Gnomad4 AMR exome AF: 0.000259

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000267

Gnomad4 SAS exome AF: 0.000265

Gnomad4 FIN exome AF: 0.0000403

Gnomad4 NFE exome AF: 0.0000952

Gnomad4 OTH exome AF: 0.000104

GnomAD4 genome AF: 0.000133 AC: 20 AN: 150672 Hom.: 0 Cov.: 0 AF XY: 0.000150 AC XY: 11 AN XY: 73550

Gnomad4 AFR AF: 0.000195

Gnomad4 AMR AF: 0.000132

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000394

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000118

Gnomad4 OTH AF: 0.00

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;