dbSNP rs1531312: MAP1B:c.286+92T>C (chr5-72115891-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005909.5(MAP1B):c.286+92T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 839,288 control chromosomes in the GnomAD database, including 194,516 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 ( 32223 hom., cov: 32)

Exomes 𝑓: 0.68 ( 162293 hom. )

Consequence

MAP1B
NM_005909.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0570

Publications

8 publications found

Variant links:

Genes affected

MAP1B (HGNC:6836): (microtubule associated protein 1B) This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The product of this gene is a precursor polypeptide that presumably undergoes proteolytic processing to generate the final MAP1B heavy chain and LC1 light chain. Gene knockout studies of the mouse microtubule-associated protein 1B gene suggested an important role in development and function of the nervous system. [provided by RefSeq, Jul 2008]

MAP1B Gene-Disease associations (from GenCC):

periventricular nodular heterotopia 9
Inheritance: AD Classification: STRONG Submitted by: Illumina, Labcorp Genetics (formerly Invitae)
periventricular nodular heterotopia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

MAP1B links:

Genome browser will be placed here

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=-0.76).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP1B	NM_005909.5 link	c.286+92T>C		intron_variant	Intron 2 of 6	ENST00000296755.12	NP_005900.2	P46821Q86X89Q6PJD3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP1B	ENST00000296755.12 link	c.286+92T>C		intron_variant	Intron 2 of 6	1	NM_005909.5	ENSP00000296755.7		P46821

Frequencies

GnomAD3 genomes

AF:

0.644

AC:

97806

AN:

151904

Hom.:

32205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.540

Gnomad AMI

AF:

0.821

Gnomad AMR

AF:

0.607

Gnomad ASJ

AF:

0.762

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.729

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.716

Gnomad OTH

AF:

0.676

GnomAD4 exome

AF:

0.680

AC:

467489

AN:

687266

Hom.:

162293

Cov.:

AF XY:

0.683

AC XY:

251082

AN XY:

367564

show subpopulations

African (AFR)

AF:

0.541

AC:

9884

AN:

18286

American (AMR)

AF:

0.597

AC:

23228

AN:

38888

Ashkenazi Jewish (ASJ)

AF:

0.769

AC:

15534

AN:

20198

East Asian (EAS)

AF:

0.341

AC:

12073

AN:

35432

South Asian (SAS)

AF:

0.659

AC:

44456

AN:

67412

European-Finnish (FIN)

AF:

0.737

AC:

35691

AN:

48454

Middle Eastern (MID)

AF:

0.742

AC:

3037

AN:

4094

European-Non Finnish (NFE)

AF:

0.714

AC:

299963

AN:

419888

Other (OTH)

AF:

0.682

AC:

23623

AN:

34614

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

6936

13871

20807

27742

34678

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3168

6336

9504

12672

15840

<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:

0.644

AC:

97878

AN:

152022

Hom.:

32223

Cov.:

AF XY:

0.641

AC XY:

47630

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.540

AC:

22375

AN:

41428

American (AMR)

AF:

0.607

AC:

9278

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.762

AC:

2644

AN:

3468

East Asian (EAS)

AF:

0.340

AC:

1759

AN:

5172

South Asian (SAS)

AF:

0.643

AC:

3096

AN:

4818

European-Finnish (FIN)

AF:

0.729

AC:

7698

AN:

10562

Middle Eastern (MID)

AF:

0.728

AC:

214

AN:

294

European-Non Finnish (NFE)

AF:

0.716

AC:

48644

AN:

67976

Other (OTH)

AF:

0.674

AC:

1423

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1717

3434

5151

6868

8585

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<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:

0.693

Hom.:

151601

Bravo

AF:

0.631

Asia WGS

AF:

0.531

AC:

1849

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

5.4

(source)

DANN

Benign

0.87

PhyloP100

-0.057

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over