NM_001364716.4:c.566_568delGCA

Variant names:

• chr17-17136247-CCAG-C
• rs3833098
• NM_001364716.4:c.566_568delGCA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP3 BP6 BA1

The NM_001364716.4(MPRIP):​c.566_568delGCA​(p.Ser189del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.72 (39080 hom., cov: 0)
  • Exomes 𝑓: 0.61 (210261 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 -10 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001364716.4
• BP6: Variant 17-17136247-CCAG-C is Benign according to our data. Variant chr17-17136247-CCAG-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4	c.566_568delGCA	p.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.566_568delGCA	p.Ser189del	disruptive_inframe_deletion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.720 AC: 108275 AN: 150448 Hom.: 39042 Cov.: 0

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.695

GnomAD3 exomes AF: 0.717 AC: 153947 AN: 214846 Hom.: 54637 AF XY: 0.718 AC XY: 83964 AN XY: 116878

Gnomad AFR exome AF: 0.653

Gnomad AMR exome AF: 0.769

Gnomad ASJ exome AF: 0.680

Gnomad EAS exome AF: 0.838

Gnomad SAS exome AF: 0.750

Gnomad FIN exome AF: 0.796

Gnomad NFE exome AF: 0.672

Gnomad OTH exome AF: 0.684

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.611 AC: 849553 AN: 1389348 Hom.: 210261 AF XY: 0.611 AC XY: 422077 AN XY: 691266

Gnomad4 AFR exome AF: 0.597

Gnomad4 AMR exome AF: 0.631

Gnomad4 ASJ exome AF: 0.575

Gnomad4 EAS exome AF: 0.684

Gnomad4 SAS exome AF: 0.602

Gnomad4 FIN exome AF: 0.656

Gnomad4 NFE exome AF: 0.609

Gnomad4 OTH exome AF: 0.602

GnomAD4 genome AF: 0.720 AC: 108367 AN: 150562 Hom.: 39080 Cov.: 0 AF XY: 0.725 AC XY: 53298 AN XY: 73488

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.694

Bravo AF: 0.739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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;