Variant chr2-71133269-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005791.3(MPHOSPH10):c.461A>G(p.Asn154Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00636 in 1,614,032 control chromosomes in the GnomAD database, including 221 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 93 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 128 hom. )

Consequence

MPHOSPH10
NM_005791.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0520

Variant links:

Genes affected

MPHOSPH10 (HGNC:7213): (M-phase phosphoprotein 10) This gene encodes a protein that is phosphorylated during mitosis. The protein localizes to the nucleolus during interphase and to the chromosomes during M phase. The protein associates with the U3 small nucleolar ribonucleoprotein 60-80S complexes and may be involved in pre-rRNA processing. [provided by RefSeq, Dec 2010]

MPHOSPH10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018321276).

BP6

Variant 2-71133269-A-G is Benign according to our data. Variant chr2-71133269-A-G is described in ClinVar as [Benign]. Clinvar id is 777994.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPHOSPH10	NM_005791.3 linkuse as main transcript	c.461A>G	p.Asn154Ser	missense_variant	2/11	ENST00000244230.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH10	ENST00000244230.7 linkuse as main transcript	c.461A>G	p.Asn154Ser	missense_variant	2/11	1	NM_005791.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0205

AC:

3122

AN:

152054

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0632

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0105

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00982

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00282

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.00826

AC:

2078

AN:

251424

Hom.:

AF XY:

0.00749

AC XY:

1018

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.0655

Gnomad AMR exome

AF:

0.00431

Gnomad ASJ exome

AF:

0.00198

Gnomad EAS exome

AF:

0.00805

Gnomad SAS exome

AF:

0.0120

Gnomad FIN exome

AF:

0.0000924

Gnomad NFE exome

AF:

0.00253

Gnomad OTH exome

AF:

0.00619

GnomAD4 exome

AF:

0.00489

AC:

7144

AN:

1461860

Hom.:

128

Cov.:

AF XY:

0.00491

AC XY:

3570

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0657

Gnomad4 AMR exome

AF:

0.00478

Gnomad4 ASJ exome

AF:

0.00126

Gnomad4 EAS exome

AF:

0.00580

Gnomad4 SAS exome

AF:

0.0125

Gnomad4 FIN exome

AF:

0.000112

Gnomad4 NFE exome

AF:

0.00245

Gnomad4 OTH exome

AF:

0.00959

GnomAD4 genome

AF:

0.0205

AC:

3124

AN:

152172

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

1416

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0631

Gnomad4 AMR

AF:

0.0105

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00984

Gnomad4 SAS

AF:

0.0127

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00282

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00582

Hom.:

Bravo

AF:

0.0242

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.0586

AC:

258

ESP6500EA

AF:

0.00302

AC:

ExAC

AF:

0.00944

AC:

1146

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.00425

EpiControl

AF:

0.00326

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 18, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.48

DANN

Benign

0.45

DEOGEN2

Benign

0.0031

T;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.085

LIST_S2

Benign

0.67

T;T

MetaRNN

Benign

0.0018

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.18

N;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.40

N;.

REVEL

Benign

0.024

Sift

Benign

0.54

T;.

Sift4G

Benign

0.71

T;T

Polyphen

0.0010

B;.

Vest4

0.046

MVP

0.33

MPC

0.098

ClinPred

0.0014

GERP RS

-0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.017

gMVP

0.018

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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