17-17136247-CCAGCAGCAG-C

Position:

• chr17-17136247-CCAGCAGCAG-C

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3 BP6_Moderate BS2

The NM_001364716.4(MPRIP):​c.560_568del​(p.Ser187_Ser189del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,555,542 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0010 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0012 (2 hom.)
• Consequence: MPRIP NM_001364716.4 inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 -7 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001364716.4
• BP6: Variant 17-17136247-CCAGCAGCAG-C is Benign according to our data. Variant chr17-17136247-CCAGCAGCAG-C is described in ClinVar as [Benign]. Clinvar id is 2672689.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPRIP	NM_001364716.4	c.560_568del	p.Ser187_Ser189del	inframe_deletion	6/24	ENST00000651222.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPRIP	ENST00000651222.2	c.560_568del	p.Ser187_Ser189del	inframe_deletion	6/24		NM_001364716.4	A2

Frequencies

GnomAD3 genomes AF: 0.00103 AC: 155 AN: 150558 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000514

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000662

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00337

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00142

Gnomad OTH AF: 0.000484

GnomAD3 exomes AF: 0.000745 AC: 160 AN: 214846 Hom.: 0 AF XY: 0.000779 AC XY: 91 AN XY: 116878

Gnomad AFR exome AF: 0.000301

Gnomad AMR exome AF: 0.000134

Gnomad ASJ exome AF: 0.000112

Gnomad EAS exome AF: 0.000143

Gnomad SAS exome AF: 0.000300

Gnomad FIN exome AF: 0.00223

Gnomad NFE exome AF: 0.000985

Gnomad OTH exome AF: 0.000383

GnomAD4 exome AF: 0.00118 AC: 1663 AN: 1404870 Hom.: 2 AF XY: 0.00119 AC XY: 835 AN XY: 698924

Gnomad4 AFR exome AF: 0.000403

Gnomad4 AMR exome AF: 0.000141

Gnomad4 ASJ exome AF: 0.000397

Gnomad4 EAS exome AF: 0.000108

Gnomad4 SAS exome AF: 0.000205

Gnomad4 FIN exome AF: 0.00391

Gnomad4 NFE exome AF: 0.00128

Gnomad4 OTH exome AF: 0.000795

GnomAD4 genome AF: 0.00102 AC: 154 AN: 150672 Hom.: 0 Cov.: 0 AF XY: 0.00105 AC XY: 77 AN XY: 73550

Gnomad4 AFR AF: 0.000488

Gnomad4 AMR AF: 0.0000661

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00337

Gnomad4 NFE AF: 0.00142

Gnomad4 OTH AF: 0.000479

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

MPRIP: BS1, BS2 -

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;