Genetic Variant MOBP:n.*1470A>G (chr3-39525645-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 ENST00000452959.6(MOBP):n.*1470A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,192 control chromosomes in the GnomAD database, including 10,512 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 0.33 ( 10506 hom., cov: 32)

Exomes 𝑓: 0.22 ( 6 hom. )

Consequence

MOBP
ENST00000452959.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.677

Publications

6 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452959.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
MOBP	NR_003090.3	n.1865A>G	non_coding_transcript_exon	Exon 6 of 6
MOBP	NR_103504.2	n.2207A>G	non_coding_transcript_exon	Exon 7 of 7
MOBP	NR_103505.2	n.2245A>G	non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOBP	ENST00000452959.6	TSL:1	n.*1470A>G		non_coding_transcript_exon	Exon 6 of 6	ENSP00000405549.1
	MOBP	ENST00000452959.6	TSL:1	n.*1470A>G		3_prime_UTR	Exon 6 of 6	ENSP00000405549.1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49331

AN:

151888

Hom.:

10475

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.303

GnomAD4 exome

AF:

0.220

AC:

AN:

186

Hom.:

Cov.:

AF XY:

0.246

AC XY:

AN XY:

122

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.182

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.218

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.325

AC:

49425

AN:

152006

Hom.:

10506

Cov.:

AF XY:

0.321

AC XY:

23824

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.612

AC:

25378

AN:

41450

American (AMR)

AF:

0.274

AC:

4184

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

903

AN:

3468

East Asian (EAS)

AF:

0.258

AC:

1330

AN:

5164

South Asian (SAS)

AF:

0.146

AC:

704

AN:

4812

European-Finnish (FIN)

AF:

0.197

AC:

2083

AN:

10566

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

14029

AN:

67948

Other (OTH)

AF:

0.304

AC:

641

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1479

2958

4438

5917

7396

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

444

888

1332

1776

2220

<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:

0.265

Hom.:

1602

Bravo

AF:

0.344

Asia WGS

AF:

0.233

AC:

812

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.7

(source)

DANN

Benign

0.85

PhyloP100

-0.68

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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