Variant 17-17136299-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001364716.4(MPRIP):c.585A>G(p.Lys195Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00198 in 1,613,800 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0020 ( 13 hom. )

Consequence

MPRIP
NM_001364716.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0280

Variant links:

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]

MPRIP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 17-17136299-A-G is Benign according to our data. Variant chr17-17136299-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2647510.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.028 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00196 (2869/1461648) while in subpopulation MID AF= 0.0248 (143/5768). AF 95% confidence interval is 0.0215. There are 13 homozygotes in gnomad4_exome. There are 1570 alleles in male gnomad4_exome subpopulation. Median coverage is 35. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 13 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4 link	c.585A>G	p.Lys195Lys	synonymous_variant	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 link	c.585A>G	p.Lys195Lys	synonymous_variant	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1		A0A494BZV2

Frequencies

GnomAD3 genomes

AF:

0.00217

AC:

330

AN:

152034

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000459

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00380

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00436

Gnomad FIN

AF:

0.00189

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00272

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00260

AC:

648

AN:

249614

Hom.:

AF XY:

0.00310

AC XY:

419

AN XY:

135064

show subpopulations

Gnomad AFR exome

AF:

0.000434

Gnomad AMR exome

AF:

0.00192

Gnomad ASJ exome

AF:

0.00200

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00468

Gnomad FIN exome

AF:

0.00144

Gnomad NFE exome

AF:

0.00296

Gnomad OTH exome

AF:

0.00789

GnomAD4 exome

AF:

0.00196

AC:

2869

AN:

1461648

Hom.:

Cov.:

AF XY:

0.00216

AC XY:

1570

AN XY:

727116

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00210

Gnomad4 ASJ exome

AF:

0.00214

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00471

Gnomad4 FIN exome

AF:

0.00122

Gnomad4 NFE exome

AF:

0.00169

Gnomad4 OTH exome

AF:

0.00305

GnomAD4 genome

AF:

0.00218

AC:

331

AN:

152152

Hom.:

Cov.:

AF XY:

0.00242

AC XY:

180

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.000482

Gnomad4 AMR

AF:

0.00379

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00478

Gnomad4 FIN

AF:

0.00189

Gnomad4 NFE

AF:

0.00272

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00288

Hom.:

Bravo

AF:

0.00251

EpiCase

AF:

0.00431

EpiControl

AF:

0.00434

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Apr 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MPRIP: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

6.0

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over