Genetic Variant MOBP:c.*667A>G (chr3-39514089-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000383754.7(MOBP):c.*667A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,028 control chromosomes in the GnomAD database, including 10,019 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 0.32 ( 10019 hom., cov: 31)

Exomes 𝑓: 0.15 ( 0 hom. )

Consequence

MOBP
ENST00000383754.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160

Publications

31 publications found

Variant links:

Genes affected

MOBP (HGNC:7189): (myelin associated oligodendrocyte basic protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be a structural constituent of myelin sheath. Predicted to be involved in nervous system development. Predicted to be located in mitochondrion. Predicted to be active in cortical actin cytoskeleton. Implicated in frontotemporal dementia. [provided by Alliance of Genome Resources, Apr 2022]

MOBP 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000383754.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
MOBP	NR_103506.2	n.852A>G	non_coding_transcript_exon	Exon 3 of 3
MOBP	NM_001278322.2	c.*706A>G	3_prime_UTR	Exon 5 of 5	NP_001265251.1
MOBP	NM_182935.4	c.*667A>G	3_prime_UTR	Exon 4 of 4	NP_891980.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MOBP	ENST00000383754.7	TSL:1	c.*667A>G	3_prime_UTR	Exon 4 of 4	ENSP00000373261.3
MOBP	ENST00000424090.5	TSL:1	n.*258+483A>G	intron	N/A	ENSP00000389055.1
MOBP	ENST00000442631.5	TSL:1	n.*223+483A>G	intron	N/A	ENSP00000413771.1

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47893

AN:

151844

Hom.:

9990

Cov.:

show subpopulations

Gnomad AFR

AF:

0.600

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.198

Gnomad OTH

AF:

0.288

GnomAD4 exome

AF:

0.147

AC:

AN:

Hom.:

Cov.:

AF XY:

0.146

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.100

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.154

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.555

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.316

AC:

47984

AN:

151960

Hom.:

10019

Cov.:

AF XY:

0.311

AC XY:

23073

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.601

AC:

24850

AN:

41378

American (AMR)

AF:

0.263

AC:

4026

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

886

AN:

3464

East Asian (EAS)

AF:

0.253

AC:

1306

AN:

5160

South Asian (SAS)

AF:

0.140

AC:

671

AN:

4810

European-Finnish (FIN)

AF:

0.188

AC:

1992

AN:

10574

Middle Eastern (MID)

AF:

0.284

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.198

AC:

13482

AN:

67966

Other (OTH)

AF:

0.288

AC:

607

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1426

2852

4277

5703

7129

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<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:

0.229

Hom.:

15807

Bravo

AF:

0.335

Asia WGS

AF:

0.223

AC:

775

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.3

(source)

DANN

Benign

0.59

PhyloP100

0.016

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over