Variant 16-82151507-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005792.2(MPHOSPH6):c.172A>G(p.Ile58Val) variant causes a missense change. The variant allele was found at a frequency of 0.0311 in 1,585,124 control chromosomes in the GnomAD database, including 942 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.026 ( 82 hom., cov: 33)

Exomes 𝑓: 0.032 ( 860 hom. )

Consequence

MPHOSPH6
NM_005792.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.32

Variant links:

Genes affected

MPHOSPH6 (HGNC:7214): (M-phase phosphoprotein 6) Predicted to enable RNA binding activity. Involved in maturation of 5.8S rRNA. Located in cytosol; nucleolus; and nucleoplasm. Colocalizes with nuclear exosome (RNase complex). [provided by Alliance of Genome Resources, Apr 2022]

MPHOSPH6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0030200183).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPHOSPH6	NM_005792.2 linkuse as main transcript	c.172A>G	p.Ile58Val	missense_variant	3/5	ENST00000258169.9
MPHOSPH6	XM_011522808.4 linkuse as main transcript	c.118A>G	p.Ile40Val	missense_variant	4/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH6	ENST00000258169.9 linkuse as main transcript	c.172A>G	p.Ile58Val	missense_variant	3/5	1	NM_005792.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0260

AC:

3960

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00613

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0274

Gnomad ASJ

AF:

0.0291

Gnomad EAS

AF:

0.0496

Gnomad SAS

AF:

0.0597

Gnomad FIN

AF:

0.0421

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0313

Gnomad OTH

AF:

0.0253

GnomAD3 exomes

AF:

0.0368

AC:

8536

AN:

232116

Hom.:

191

AF XY:

0.0375

AC XY:

4729

AN XY:

126014

show subpopulations

Gnomad AFR exome

AF:

0.00551

Gnomad AMR exome

AF:

0.0466

Gnomad ASJ exome

AF:

0.0319

Gnomad EAS exome

AF:

0.0440

Gnomad SAS exome

AF:

0.0562

Gnomad FIN exome

AF:

0.0421

Gnomad NFE exome

AF:

0.0322

Gnomad OTH exome

AF:

0.0354

GnomAD4 exome

AF:

0.0316

AC:

45273

AN:

1432850

Hom.:

860

Cov.:

AF XY:

0.0326

AC XY:

23161

AN XY:

711064

show subpopulations

Gnomad4 AFR exome

AF:

0.00436

Gnomad4 AMR exome

AF:

0.0432

Gnomad4 ASJ exome

AF:

0.0283

Gnomad4 EAS exome

AF:

0.0507

Gnomad4 SAS exome

AF:

0.0550

Gnomad4 FIN exome

AF:

0.0409

Gnomad4 NFE exome

AF:

0.0293

Gnomad4 OTH exome

AF:

0.0297

GnomAD4 genome

AF:

0.0260

AC:

3964

AN:

152274

Hom.:

Cov.:

AF XY:

0.0271

AC XY:

2020

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00611

Gnomad4 AMR

AF:

0.0274

Gnomad4 ASJ

AF:

0.0291

Gnomad4 EAS

AF:

0.0497

Gnomad4 SAS

AF:

0.0599

Gnomad4 FIN

AF:

0.0421

Gnomad4 NFE

AF:

0.0313

Gnomad4 OTH

AF:

0.0265

Alfa

AF:

0.0296

Hom.:

153

Bravo

AF:

0.0234

TwinsUK

AF:

0.0256

AC:

ALSPAC

AF:

0.0296

AC:

114

ESP6500AA

AF:

0.00705

AC:

ESP6500EA

AF:

0.0313

AC:

268

ExAC

AF:

0.0370

AC:

4494

Asia WGS

AF:

0.0540

AC:

186

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.33

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0056

T;.

Eigen

Uncertain

0.46

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.85

D;D

MetaRNN

Benign

0.0030

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.4

M;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.57

PROVEAN

Benign

-0.45

N;N

REVEL

Benign

0.10

Sift

Benign

0.17

T;T

Sift4G

Benign

0.73

T;T

Polyphen

0.91

P;.

Vest4

0.43

MPC

0.0055

ClinPred

0.031

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.29

gMVP

0.24

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over