Variant rs1051431 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_022782.4(MPHOSPH9):c.3261C>T(p.Tyr1087Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,613,812 control chromosomes in the GnomAD database, including 473,646 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 0.64 ( 35267 hom., cov: 31)

Exomes 𝑓: 0.77 ( 438379 hom. )

Consequence

MPHOSPH9
NM_022782.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.399

Variant links:

Genes affected

MPHOSPH9 (HGNC:7215): (M-phase phosphoprotein 9) Located in Golgi apparatus and centriole. Implicated in multiple sclerosis. [provided by Alliance of Genome Resources, Apr 2022]

MPHOSPH9 links:

MPHOSPH9 (HGNC:):

MPHOSPH9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=-0.399 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MPHOSPH9	NM_022782.4 linkuse as main transcript	c.3261C>T	p.Tyr1087Tyr	synonymous_variant	22/24	ENST00000606320.6	NP_073619.3	Q99550

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPHOSPH9	ENST00000606320.6 linkuse as main transcript	c.3261C>T	p.Tyr1087Tyr	synonymous_variant	22/24	5	NM_022782.4	ENSP00000475489.1		Q99550

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

96580

AN:

151944

Hom.:

35257

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.827

Gnomad AMR

AF:

0.737

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.972

Gnomad SAS

AF:

0.731

Gnomad FIN

AF:

0.802

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.673

GnomAD3 exomes

AF:

0.742

AC:

186445

AN:

251428

Hom.:

72169

AF XY:

0.749

AC XY:

101774

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.232

Gnomad AMR exome

AF:

0.725

Gnomad ASJ exome

AF:

0.688

Gnomad EAS exome

AF:

0.974

Gnomad SAS exome

AF:

0.727

Gnomad FIN exome

AF:

0.807

Gnomad NFE exome

AF:

0.777

Gnomad OTH exome

AF:

0.760

GnomAD4 exome

AF:

0.769

AC:

1123368

AN:

1461750

Hom.:

438379

Cov.:

AF XY:

0.768

AC XY:

558210

AN XY:

727190

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.725

Gnomad4 ASJ exome

AF:

0.689

Gnomad4 EAS exome

AF:

0.975

Gnomad4 SAS exome

AF:

0.725

Gnomad4 FIN exome

AF:

0.807

Gnomad4 NFE exome

AF:

0.784

Gnomad4 OTH exome

AF:

0.751

GnomAD4 genome

AF:

0.635

AC:

96615

AN:

152062

Hom.:

35267

Cov.:

AF XY:

0.642

AC XY:

47742

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.251

Gnomad4 AMR

AF:

0.736

Gnomad4 ASJ

AF:

0.669

Gnomad4 EAS

AF:

0.972

Gnomad4 SAS

AF:

0.732

Gnomad4 FIN

AF:

0.802

Gnomad4 NFE

AF:

0.783

Gnomad4 OTH

AF:

0.676

Alfa

AF:

0.739

Hom.:

54840

Bravo

AF:

0.611

Asia WGS

AF:

0.821

AC:

2852

AN:

3478

EpiCase

AF:

0.765

EpiControl

AF:

0.770

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.1

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over