NM_052845.4:c.57C>A

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_052845.4(MMAB):c.57C>A(p.Arg19Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,607,664 control chromosomes in the GnomAD database, including 60,800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7459 hom., cov: 33)

Exomes 𝑓: 0.27 ( 53341 hom. )

Consequence

MMAB
NM_052845.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:14

Conservation

PhyloP100: -0.0470

Variant links:

Genes affected

MMAB (HGNC:19331): (metabolism of cobalamin associated B) This gene encodes a protein that catalyzes the final step in the conversion of vitamin B(12) into adenosylcobalamin (AdoCbl), a vitamin B12-containing coenzyme for methylmalonyl-CoA mutase. Mutations in the gene are the cause of vitamin B12-dependent methylmalonic aciduria linked to the cblB complementation group. Alternatively spliced transcript variants have been found. [provided by RefSeq, Apr 2011]

MMAB links:

MVK (HGNC:7530): (mevalonate kinase) This gene encodes the peroxisomal enzyme mevalonate kinase. Mevalonate is a key intermediate, and mevalonate kinase a key early enzyme, in isoprenoid and sterol synthesis. Mevalonate kinase deficiency caused by mutation of this gene results in mevalonic aciduria, a disease characterized psychomotor retardation, failure to thrive, hepatosplenomegaly, anemia and recurrent febrile crises. Defects in this gene also cause hyperimmunoglobulinaemia D and periodic fever syndrome, a disorder characterized by recurrent episodes of fever associated with lymphadenopathy, arthralgia, gastrointestinal dismay and skin rash. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

MVK links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 12-109573424-G-T is Benign according to our data. Variant chr12-109573424-G-T is described in ClinVar as [Benign]. Clinvar id is 262247.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-109573424-G-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.047 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMAB	NM_052845.4 link	c.57C>A	p.Arg19Arg	synonymous_variant	Exon 1 of 9	ENST00000545712.7	NP_443077.1	Q96EY8
MVK	XM_047428873.1 link	c.139G>T	p.Ala47Ser	missense_variant	Exon 1 of 11		XP_047284829.1
MVK	XM_017019313.3 link	c.-162G>T		5_prime_UTR_variant	Exon 1 of 10		XP_016874802.1	F5H8H2
MMAB	NR_038118.2 link	n.81C>A		non_coding_transcript_exon_variant	Exon 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMAB	ENST00000545712.7 link	c.57C>A	p.Arg19Arg	synonymous_variant	Exon 1 of 9	1	NM_052845.4	ENSP00000445920.1		Q96EY8

Frequencies

GnomAD3 genomes

AF:

0.307

AC:

46640

AN:

151714

Hom.:

7423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.317

GnomAD3 exomes

AF:

0.269

AC:

63010

AN:

234304

Hom.:

8743

AF XY:

0.266

AC XY:

34148

AN XY:

128616

show subpopulations

Gnomad AFR exome

AF:

0.415

Gnomad AMR exome

AF:

0.273

Gnomad ASJ exome

AF:

0.299

Gnomad EAS exome

AF:

0.125

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.276

Gnomad OTH exome

AF:

0.270

GnomAD4 exome

AF:

0.266

AC:

387968

AN:

1455832

Hom.:

53341

Cov.:

AF XY:

0.267

AC XY:

193153

AN XY:

724124

show subpopulations

Gnomad4 AFR exome

AF:

0.412

Gnomad4 AMR exome

AF:

0.283

Gnomad4 ASJ exome

AF:

0.292

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.230

Gnomad4 FIN exome

AF:

0.297

Gnomad4 NFE exome

AF:

0.267

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.308

AC:

46726

AN:

151832

Hom.:

7459

Cov.:

AF XY:

0.306

AC XY:

22691

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.401

Gnomad4 AMR

AF:

0.294

Gnomad4 ASJ

AF:

0.281

Gnomad4 EAS

AF:

0.133

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.314

Alfa

AF:

0.266

Hom.:

2788

Bravo

AF:

0.314

Asia WGS

AF:

0.184

AC:

640

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:14

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Aug 19, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

Methylmalonic aciduria, cblB type

Benign:4

Sep 16, 2020

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 09, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mevalonic aciduria

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Methylmalonic acidemia

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hyperimmunoglobulin D with periodic fever

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

5.9

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over