Genetic Variant NM_005791.3:c.122C>A (chr2-71132930-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_005791.3(MPHOSPH10):c.122C>A(p.Ser41Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00625 in 1,610,868 control chromosomes in the GnomAD database, including 217 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 91 hom., cov: 32)

Exomes 𝑓: 0.0048 ( 126 hom. )

Consequence

MPHOSPH10
NM_005791.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.90

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=0.0029021204).

BP6

Variant 2-71132930-C-A is Benign according to our data. Variant chr2-71132930-C-A is described in ClinVar as [Benign]. Clinvar id is 777993.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.061 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPHOSPH10	NM_005791.3 link	c.122C>A	p.Ser41Tyr	missense_variant	Exon 2 of 11	ENST00000244230.7	NP_005782.1	O00566

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPHOSPH10	ENST00000244230.7 link	c.122C>A	p.Ser41Tyr	missense_variant	Exon 2 of 11	1	NM_005791.3	ENSP00000244230.2		O00566

Frequencies

GnomAD3 genomes

AF:

0.0205

AC:

3121

AN:

152100

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0631

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0105

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00980

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00282

Gnomad OTH

AF:

0.0162

GnomAD3 exomes

AF:

0.00805

AC:

1999

AN:

248250

Hom.:

AF XY:

0.00744

AC XY:

1004

AN XY:

135032

show subpopulations

Gnomad AFR exome

AF:

0.0662

Gnomad AMR exome

AF:

0.00428

Gnomad ASJ exome

AF:

0.00201

Gnomad EAS exome

AF:

0.00796

Gnomad SAS exome

AF:

0.0120

Gnomad FIN exome

AF:

0.0000926

Gnomad NFE exome

AF:

0.00252

Gnomad OTH exome

AF:

0.00613

GnomAD4 exome

AF:

0.00476

AC:

6937

AN:

1458650

Hom.:

126

Cov.:

AF XY:

0.00479

AC XY:

3474

AN XY:

725290

show subpopulations

Gnomad4 AFR exome

AF:

0.0642

Gnomad4 AMR exome

AF:

0.00473

Gnomad4 ASJ exome

AF:

0.00127

Gnomad4 EAS exome

AF:

0.00575

Gnomad4 SAS exome

AF:

0.0124

Gnomad4 FIN exome

AF:

0.000112

Gnomad4 NFE exome

AF:

0.00236

Gnomad4 OTH exome

AF:

0.00931

GnomAD4 genome

AF:

0.0205

AC:

3123

AN:

152218

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

1417

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0630

Gnomad4 AMR

AF:

0.0105

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00983

Gnomad4 SAS

AF:

0.0127

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00282

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00993

Hom.:

Bravo

AF:

0.0242

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.0524

AC:

226

ESP6500EA

AF:

0.00281

AC:

ExAC

AF:

0.00902

AC:

1093

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.00420

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 18, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Benign

0.80

DEOGEN2

Benign

0.017

T;T

Eigen

Benign

-0.094

Eigen_PC

Benign

-0.0067

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.78

T;T

MetaRNN

Benign

0.0029

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.0

M;.

PrimateAI

Benign

0.41

PROVEAN

Uncertain

-2.7

D;.

REVEL

Benign

0.13

Sift

Benign

0.43

T;.

Sift4G

Uncertain

0.025

D;D

Polyphen

0.015

B;.

Vest4

0.23

MVP

0.34

MPC

0.21

ClinPred

0.022

GERP RS

3.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.11

gMVP

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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