Genetic Variant MPHOSPH10:c.1666-152C>T (chr2-71149071-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005791.3(MPHOSPH10):c.1666-152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 663,194 control chromosomes in the GnomAD database, including 83,211 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 16002 hom., cov: 33)

Exomes 𝑓: 0.51 ( 67209 hom. )

Consequence

MPHOSPH10
NM_005791.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.167

Publications

9 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005791.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPHOSPH10	NM_005791.3	MANE Select	c.1666-152C>T		intron	N/A	NP_005782.1	O00566

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MPHOSPH10	ENST00000244230.7	TSL:1 MANE Select	c.1666-152C>T	intron	N/A	ENSP00000244230.2	O00566
MPHOSPH10	ENST00000857231.1		c.1612-152C>T	intron	N/A	ENSP00000527290.1
MPHOSPH10	ENST00000931987.1		c.1555-152C>T	intron	N/A	ENSP00000602046.1

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

67293

AN:

151964

Hom.:

15999

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.487

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.537

Gnomad OTH

AF:

0.473

GnomAD4 exome

AF:

0.506

AC:

258661

AN:

511112

Hom.:

67209

Cov.:

AF XY:

0.508

AC XY:

136211

AN XY:

268340

show subpopulations

African (AFR)

AF:

0.263

AC:

3492

AN:

13280

American (AMR)

AF:

0.440

AC:

8270

AN:

18806

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

8317

AN:

14072

East Asian (EAS)

AF:

0.295

AC:

9323

AN:

31602

South Asian (SAS)

AF:

0.508

AC:

22875

AN:

45028

European-Finnish (FIN)

AF:

0.505

AC:

22151

AN:

43868

Middle Eastern (MID)

AF:

0.562

AC:

1178

AN:

2096

European-Non Finnish (NFE)

AF:

0.538

AC:

169073

AN:

314416

Other (OTH)

AF:

0.500

AC:

13982

AN:

27944

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

6412

12825

19237

25650

32062

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1380

2760

4140

5520

6900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.443

AC:

67315

AN:

152082

Hom.:

16002

Cov.:

AF XY:

0.441

AC XY:

32783

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.273

AC:

11320

AN:

41476

American (AMR)

AF:

0.438

AC:

6695

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.594

AC:

2060

AN:

3470

East Asian (EAS)

AF:

0.266

AC:

1373

AN:

5168

South Asian (SAS)

AF:

0.488

AC:

2347

AN:

4814

European-Finnish (FIN)

AF:

0.511

AC:

5397

AN:

10560

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.537

AC:

36515

AN:

67998

Other (OTH)

AF:

0.476

AC:

1005

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1847

3694

5542

7389

9236

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.504

Hom.:

63262

Bravo

AF:

0.428

Asia WGS

AF:

0.377

AC:

1312

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.8

(source)

DANN

Benign

0.53

PhyloP100

0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over